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bradner lab computation pipeline scripts

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722 Commits
annotation
annotation
 
 
bamliquidator_internal
bamliquidator_internal
 
 
crc
crc
 
 
hockeysticks
hockeysticks
 
 
.gitignore
.gitignore
 
 
.pylintrc
.pylintrc
 
 
.travis.yml
.travis.yml
 
 
GPL16043.py
GPL16043.py
 
 
GPL16043.r
GPL16043.r
 
 
GPL16043.sh
GPL16043.sh
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
RNA_SEQ_PIPELINE_README.txt
RNA_SEQ_PIPELINE_README.txt
 
 
ROSE2_META.py
ROSE2_META.py
 
 
ROSE2_callSuper.R
ROSE2_callSuper.R
 
 
ROSE2_geneMapper.py
ROSE2_geneMapper.py
 
 
ROSE2_main.py
ROSE2_main.py
 
 
ROSE2_stitchOpt.R
ROSE2_stitchOpt.R
 
 
TFbridge.R
TFbridge.R
 
 
bamPlot.R
bamPlot.R
 
 
bamPlot.py
bamPlot.py
 
 
bamPlotExample.sh
bamPlotExample.sh
 
 
bamPlot_turbo.R
bamPlot_turbo.R
 
 
bamPlot_turbo.py
bamPlot_turbo.py
 
 
bamTableUpdate.py
bamTableUpdate.py
 
 
bamToGFF.py
bamToGFF.py
 
 
bamToGFFExample.sh
bamToGFFExample.sh
 
 
bamToGFF_turbo.py
bamToGFF_turbo.py
 
 
bamliquidator_batch.py
bamliquidator_batch.py
 
 
callBowtie.py
callBowtie.py
 
 
callBowtie2.py
callBowtie2.py
 
 
callBowtie2Slurm.py
callBowtie2Slurm.py
 
 
clusterEnhancer.R
clusterEnhancer.R
 
 
clusterEnhancer.py
clusterEnhancer.py
 
 
commandline_template.py
commandline_template.py
 
 
dynamicEnhancer.py
dynamicEnhancer.py
 
 
dynamicEnhancer_meta.py
dynamicEnhancer_meta.py
 
 
dynamicEnhancer_plot.R
dynamicEnhancer_plot.R
 
 
dynamicEnhancer_rank.R
dynamicEnhancer_rank.R
 
 
dynamicEnhancer_region.R
dynamicEnhancer_region.R
 
 
enhancerPromoter.py
enhancerPromoter.py
 
 
enhancerPromoter_NES.R
enhancerPromoter_NES.R
 
 
enhancerPromoter_gsea.R
enhancerPromoter_gsea.R
 
 
enhancerPromoter_waterfall.R
enhancerPromoter_waterfall.R
 
 
extractGuides.py
extractGuides.py
 
 
heatMapOrdered.R
heatMapOrdered.R
 
 
makeBamMeta.py
makeBamMeta.py
 
 
normalizeRNASeq.R
normalizeRNASeq.R
 
 
pipeline.py
pipeline.py
 
 
pipeline_dfci.py
pipeline_dfci.py
 
 
pipeline_template.py
pipeline_template.py
 
 
pipeline_template_new.py
pipeline_template_new.py
 
 
processGeckoBam.py
processGeckoBam.py
 
 
process_chiprx_sam.py
process_chiprx_sam.py
 
 
pythonTemplate.py
pythonTemplate.py
 
 
python_template.py
python_template.py
 
 
tophatTemplate.sh
tophatTemplate.sh
 
 
utils.py
utils.py
 
 

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pipeline

bradner lab computation pipeline scripts

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Copyright (c) 2013 Charles Lin and collaborators:

  • John DiMatteo
  • Nick Semenkovich
  • Xin Zhong

License: MIT (see LICENSE for details)

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bradner lab computation pipeline scripts

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  • Python 74.5%
  • R 11.3%
  • JavaScript 7.9%
  • C++ 3.4%
  • Shell 1.0%
  • HTML 0.8%
  • Other 1.1%