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tagmapAnalyseR

Version 1.0.0, released 20 April 2022.

Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.

Background

TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).

Usage

Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.

Installation

devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")

Load processed read coverage of (putative) integrations

dt<-tagmapAnalyseR::readPutativeInsertions(input)

Obtain integrations with ambiguous read coverage

ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)

Map integrations

mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)

Contact / Support

Reach out through the issues section or reach out directly to the author.

About

tagmapAnalyseR package for transposon integration mapping (TagMap).

Resources

Readme
Activity

Stars

1 star

Watchers

1 watching

Forks

2 forks
Report repository

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GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
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tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
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Packages
Contributors
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GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
Skip to content
BranchesTags
Repository files navigation
tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages

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var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
Skip to content
BranchesTags
Repository files navigation
tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages

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GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
Skip to content
BranchesTags
Repository files navigation
tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
Skip to content
BranchesTags
Repository files navigation
tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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GitHub - krademaker/tagmapAnalyseR: tagmapAnalyseR package for transposon integration mapping (TagMap). · GitHub
Skip to content
BranchesTags
Repository files navigation
tagmapAnalyseR 
Version 1.0.0, released 20 April 2022.
Stand-alone package integrated into transposon mapping pipeline tagmap_hopping for Tagmentation-Based Mapping (Tagmap) data, as well as stand-alone functionality.
Background
TagmapAnalyseR is a module inside the tagmap_hopping pipeline, and is particularly responsible to map (processed) TagMap reads to genomic locations and figure out where transposons (e.g. PiggyBac or Sleeping Beauty) integrated into the genome. TagmapAnalyseR combines several tricks to derive a consensus mapping location for integrations are read coverage may be ambiguous towards the precise location. More details can be obtained from the author upon request (methods section in thesis).
Usage
Dependencies for pipeline are described in the respective repository, see its map_insertions.R script for practical application of tagmapAnalyseR.
Installation
devtools::install_github("https://github.com/krademaker/tagmapAnalyseR")
Load processed read coverage of (putative) integrations
dt<-tagmapAnalyseR::readPutativeInsertions(input)
Obtain integrations with ambiguous read coverage
ambiguous<-tagmapAnalyseR::findAmbiguousInsertionSites(dt, padding= (nchar(overhang_sequence)*2)+2)
Map integrations
mapped<-tagmapAnalyseR::mapInsertionSites(dt=dt,
bam=bam_path,
overhang=overhang_sequence,
samtoolsPath=samtools_path,
depth= as.integer(minimal_read_depth),
ambiguousInsertions=ambiguous)
Contact / Support
Reach out through the issues section or reach out directly to the author.
About
tagmapAnalyseR package for transposon integration mapping (TagMap).
Resources
Readme
Activity
Stars
1 star
Watchers
1 watching
Forks
2 forks
Report repository
Releases
Packages
Contributors
Languages