pipeline

bradner lab computation pipeline scripts

John DiMatteo
Nick Semenkovich
Xin Zhong

License: MIT (see LICENSE for details)

Name		Name	Last commit message	Last commit date
Latest commit History 714 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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