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mikewolfe
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ChIPseq_pipeline
A general ChIP-seq pipeline to reproducibly process many samples at once.
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Update to 0.3.0
#33
mikewolfe
closed
1 year ago
0
Add motif calling and update peak calling
#32
mikewolfe
closed
2 years ago
0
Add bwtools_multicompare for collapsing bw files into one
#31
mikewolfe
closed
2 years ago
0
Add support for single end libraries
#30
mikewolfe
closed
2 years ago
0
Add region-based summary calculations for RNAP ChIP
#29
mikewolfe
closed
2 years ago
0
Allow mixing of scaling methods
#28
mikewolfe
closed
2 years ago
0
Add a summary table to variant calling
#27
mikewolfe
closed
3 years ago
0
Add variant calling with `breseq` and NaN filters in summaries
#26
mikewolfe
closed
3 years ago
1
Add variant calling rule
#25
mikewolfe
closed
3 years ago
0
Add spike-in normalization. Update genbank parsing.
#24
mikewolfe
closed
3 years ago
0
Add spike-in norm
#23
mikewolfe
closed
3 years ago
0
Add support for ratios without log transformations. Version 0.2.1
#22
mikewolfe
closed
3 years ago
0
Update Multiqc to deal with sample names more cleanly
#21
mikewolfe
closed
3 years ago
0
Add support for subtracting rather than dividing input samples
#20
mikewolfe
closed
3 years ago
0
Release 0.1.0
#19
mikewolfe
closed
3 years ago
0
Issue with development pipeline branch, cmartt peak calling
#18
cmhustmyer
closed
3 years ago
1
Update numpy in peak_calling environment
#17
mikewolfe
closed
3 years ago
0
Error in macs2_peakcalling on test
#16
cmhustmyer
closed
3 years ago
3
Add postprocessing module
#15
mikewolfe
closed
3 years ago
0
Add ability to do summaries over regions or at specified locations
#14
mikewolfe
closed
3 years ago
0
Add support for known background-based normalization
#13
mikewolfe
closed
3 years ago
0
Add ability to mask regions of the genome from analysis
#12
mikewolfe
closed
3 years ago
0
Allow for a "masked" region of the genome when performing alignments/coverage calculations
#11
mikewolfe
closed
3 years ago
0
Multiqc report is not linking files for each sample together very well
#10
mikewolfe
closed
3 years ago
0
Not urgent: New error in quality_control
#9
cmhustmyer
closed
3 years ago
2
Automatically parse genbanks for features and output into a .gff
#8
mikewolfe
closed
3 years ago
0
add MOSAiCs peak calling algorithm option
#7
cmhustmyer
opened
3 years ago
1
Allow for normalization based on a specified known background area of the chromosome
#6
mikewolfe
closed
3 years ago
0
Allow for the pipeline to run on reference genomes with more than one contig
#5
mikewolfe
closed
3 years ago
1
Change output file ending in rule run_coverage_and_norm
#4
mikewolfe
closed
3 years ago
0
Bug in running coverage and norm post-cleaning coverage and norm core
#3
cmhustmyer
closed
3 years ago
1
Add bre-seq to automatically run on input samples
#2
mikewolfe
closed
3 years ago
0
Make clean commands also clear dependent downstream calculations
#1
mikewolfe
opened
3 years ago
0