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OpenOmics
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chrom-seek
An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
https://openomics.github.io/chrom-seek/
MIT License
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Diff bind reorg
#49
rroutsong
opened
2 days ago
0
Workaround in case raw fastqs are gone and new contrasts are needed.
#48
tovahmarkowitz
opened
1 week ago
0
Updating format of the sample sheet
#47
skchronicles
opened
1 week ago
1
ppqt related issues
#46
tovahmarkowitz
opened
1 month ago
0
Diff bind reorg
#45
rroutsong
closed
2 days ago
1
Expand dba rules
#44
rroutsong
closed
2 months ago
0
split DiffBind and DiffBind block into two separate runs so Diffbind block errors don't make the DiffBind results disappear
#43
rroutsong
opened
2 months ago
0
fix: add time stamp to slurm out and err logs
#42
rroutsong
closed
2 months ago
0
Refactor codebase
#41
rroutsong
closed
2 months ago
0
ATAC Conditional Rules
#40
schaughencyp
closed
1 month ago
0
ATAC ppqt
#39
schaughencyp
closed
1 month ago
1
Adding memory for diffbind jobs
#38
tovahmarkowitz
closed
6 months ago
0
Adding new DiffBindQC for cfChIP
#37
tovahmarkowitz
closed
7 months ago
0
Adding new DiffBind QC Rmd for cfChIP and a few other DiffBind updates
#36
tovahmarkowitz
closed
7 months ago
0
add blocking to the diffbind csv prep
#35
tovahmarkowitz
closed
7 months ago
0
Add FRIP heatmap plot
#34
tovahmarkowitz
opened
7 months ago
0
Additional functionality for cfChIP
#33
tovahmarkowitz
closed
1 month ago
0
Add rerun triggers to run sub command
#32
skchronicles
opened
7 months ago
0
DiffBind block
#31
tovahmarkowitz
opened
7 months ago
0
Update Snakefile
#30
tovahmarkowitz
closed
8 months ago
0
Update behavior --peakcall parser and validation
#29
skchronicles
opened
9 months ago
0
Missing R package due to singularity sharing filesystems from host
#28
skchronicles
closed
8 months ago
2
adding DiffBind with blocking functionality
#27
asyakhl
closed
10 months ago
0
adding chip motif analysis tool, MEME rule
#26
asyakhl
closed
11 months ago
2
adding no input control functionality
#25
asyakhl
closed
11 months ago
0
Kraken and Peakcallers for single-end data
#24
asyakhl
closed
11 months ago
0
Ppqt and bam2bw rules for paired- and single-end data
#23
asyakhl
closed
1 year ago
0
trim, bwa, and deduplication rules updated to work with single-end data
#22
asyakhl
closed
1 year ago
2
SICER2 does not support rheMac10 out of the box
#21
skchronicles
opened
1 year ago
0
Empty test files
#20
prc992
closed
11 months ago
2
ppqt rule needs improved fix
#19
asyakhl
closed
11 months ago
1
Peak calling with samples lacking input controls
#18
tovahmarkowitz
closed
11 months ago
1
Adjust pipeline to work with single-end sequencing data for ChIP
#17
asyakhl
closed
11 months ago
0
add a few extra cfChIP rules
#16
asyakhl
closed
1 year ago
1
add FRiP rule
#15
asyakhl
closed
1 year ago
1
Add Homer_motif rule
#14
asyakhl
opened
1 year ago
0
add other peakcallers: macsBroad and sicer
#13
asyakhl
closed
1 year ago
1
set up pipeline to work with RheMac10 references
#12
asyakhl
closed
1 year ago
1
Build docker image for pipeline
#11
skchronicles
opened
1 year ago
0
Write script for new genome reference builds
#10
tovahmarkowitz
closed
1 year ago
0
Script to build new reference files
#9
skchronicles
opened
1 year ago
0
test ChIP-seq assay with hg38 references
#8
asyakhl
closed
1 year ago
1
test ChIP-seq assay with mm10 references
#7
asyakhl
closed
1 year ago
1
add genrich to ATAC assay
#6
asyakhl
closed
1 year ago
1
comment/document pipeline rules
#5
asyakhl
opened
1 year ago
0
test out bulk ChIP-seq assay part of the pipeline
#4
asyakhl
closed
1 year ago
1
update UROPA rule to work for cfChIP assay: basic functional cfChIP pipeline
#3
asyakhl
closed
1 year ago
1
update DiffBind rule to work
#2
asyakhl
closed
1 year ago
0
DiffBind, ngsqc, and ppqt scripts updates
#1
tovahmarkowitz
closed
1 year ago
0