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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

About

SCDC

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, '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('^' + ".*" + '
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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

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SCDC

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, '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('^' + ".*" + '
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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

About

SCDC

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, '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

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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

About

SCDC

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, '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('^' + ".*" + '
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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

About

SCDC

Resources

Stars

0 stars

Watchers

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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('^' + ".*" + '
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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

About

SCDC

Resources

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SCDC: Bulk Gene Expression Deconvolution by Multiple Single-Cell RNA Sequencing References

Travis build statusCRAN status

SCDC is a deconvolution method for bulk RNA-seq that leverages cell-type specific gene expressions from multiple scRNA-seq reference datasets. SCDC adopts an ENSEMBLE method to integrate deconvolution results from different scRNA-seq datasets that are produced in different laboratories and at different times, implicitly addressing the batch-effect confounding.

SCDC framework

Citation

Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M Perou, Fei Zou, Yuchao Jiang, SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references, Briefings in Bioinformatics, , bbz166, https://doi.org/10.1093/bib/bbz166

Installation

You can install the released version of SCDC from GitHub with:

if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("meichendong/SCDC")

Dependency package problem regarding to 'xbioc' could be resolved by:

install.packages("remotes")
remotes::install_github("renozao/xbioc")

Vignettes

Please see the vignettes page.

The SCDC paper is published at Briefings In Bioinformatics.

Questions regarding to the package can be emailed to: meichen@live.unc.edu

FAQs / Notes

  • When there is only 'one subject/individual' in the single cell dataset, please use SCDC_qc_ONE(), SCDC_prop_ONE() functions.

Aspects that could affect the deconvolution results:

  • data format: are bulk and single cell samples both raw counts / same format? We expect the data format to be consistent and comparable.
  • gene filtering: did you filter out lowly expressed genes / ribosomal genes / mitochondrial genes? These genes may affect the downstream analysis.
  • cell size and library size factors: for a single cell, do you think the sum of all gene counts (the library size) could reflect its real cell size? This is one of our assumptions: the ratio of library sizes between cell types can reflect the ratio of real cell sizes between cell types. If not, you can manually input the cell size factor when constructing the "basis matrix".
  • similar cell types: are there cell types that could potentially confound the analysis? For example, cell types that have very similar profiles /marker genes.
  • missing major cell types / technical issues: do you expect the sequencing procedure to make a big difference in bulk and sc even the technique is the same? Sometimes single cell reference data may lose information for some cell types. For example, there's fat cells in your bulk samples, but somehow you don't have it for single cell data.
  • deconvolution using a single reference dataset: did you try to use one reference dataset to test if the results make sense generally? I see you tried Bisque. Have you tried other methods like CIBERSORTx? If results from other "one-reference" deconvolution methods make more sense, then you can input these directly using our ENSEMBLE step.

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