BranchesTags

Latest commit

History

3 Commits

Folders and files

NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh

Repository files navigation

Scripts_for_Apollo

1. Running inferCNV in parallel on multiple samples using SBATCH array

anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh

Requires these files:

  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)

InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.

InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.

InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.

InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.

InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)

2. Installing BETSY on Apollo

  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.

About

No description, website, or topics provided.

Resources

Readme
GPL-3.0 license
Activity
Custom properties

Stars

0 stars

Watchers

3 watching

Forks

0 forks
Report repository

Releases

Packages

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
BranchesTags
Latest commit
History
3 Commits
Folders and files
NameName
Last commit message
Last commit date
Export_ID.r
Export_ID.r
Export_ID.sh
Export_ID.sh
FEL_annot.R
FEL_annot.R
FEL_annot_mod.r
FEL_annot_mod.r
InferCNV.R
InferCNV.R
InferCNV.batch.sh
InferCNV.batch.sh
InferCNV.create.jobs.sh
InferCNV.create.jobs.sh
InferCNV_Custom_Heatmap.R
InferCNV_Custom_Heatmap.R
InferCNV_make_counts_from_integrated_Seurat.R
InferCNV_make_counts_from_integrated_Seurat.R
LICENSE
LICENSE
README.md
README.md
Slice_SVM.sh
Slice_SVM.sh
batch_export_ID.sh
batch_export_ID.sh
batch_phylo_filter.sh
batch_phylo_filter.sh
batch_phylo_tree.sh
batch_phylo_tree.sh
batch_slice_SVM.sh
batch_slice_SVM.sh
phylo.filter.sh
phylo.filter.sh
phylo.filter_single_sample.sh
phylo.filter_single_sample.sh
phylo.tree.sh
phylo.tree.sh
phylofilter.create.jobs.sh
phylofilter.create.jobs.sh
Repository files navigation
Scripts_for_Apollo
1. Running inferCNV in parallel on multiple samples using SBATCH array
anath@ppxhpcacc01$ bash InferCNV.create.jobs.sh
Requires these files:
  1. Raw (filtered) counts file: SAMPLE.ic.counts.txt
  2. InferCNV annotations file (label anticipated cancer cells as "malignant": SAMPLE.ic.annot.txt
  3. sample.ic.txt: contains a list of SAMPLE
  4. hg19.RefSeq.NM_pos_unique_sort.txt: gene order file (static for each run)
InferCNV.create.jobs.sh creates an array of N jobs and invokes InferCNV.batch.sh. Modify N based on number of samples you will be submitting.
InferCNV.batch.sh is the actual job submission script. Modify the SBATCH parameters as required.
InferCNV.R is the R-script calling InferCNV code. Modify the path to the Conda enviroment and parmeters for InferCNV::run() based on requirements. The script will rename all non-malignant cells as "normal" in the annotations file.
InferCNV_Custom_Heatmap.R can be used to display additional gene-level annotations from raw counts, Seurat annotations and perform clustering and cut tree for displaying on complex heatmaps.
InferCNV_make_counts_from_integrated_Seurat.R can be used to export counts and annotations from an integrated Seurat object. The integrated Seurat object should contain counts after QC (i.e. after removal of low quality cells, doublets etc.)
2. Installing BETSY on Apollo
  1. Clone repository from Megatron to Apollo via Tikvah.
  2. Create a conda environment with python 2.7.
  3. Activate conda environment and install required packages listed in README.
  4. Run python setup.py build and python setup.py install.
  5. Copy required Singularity containers from Megatron to Apollo via Tikvah.
  6. Follow instructions in README to set paths to the executables and Singularity containers in ~/.genomicoderc and ~/.betsyrc.
About
No description, website, or topics provided.
Resources
Readme
GPL-3.0 license
Activity
Custom properties
Stars
0 stars
Watchers
3 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages