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lcdb
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lcdb-wf
Robust, tested workflows for RNA-seq, ChIP-seq and other high-throughput sequencing analysis
https://lcdb.github.io/lcdb-wf
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Change SRA fastq directory
#418
b-full
opened
1 day ago
0
add Plodia interpunctella reference config
#417
daler
closed
2 days ago
0
V1.12rc
#416
daler
opened
1 week ago
0
Make strand_arg a param
#415
b-full
closed
1 week ago
0
Make strand_arg a param
#414
b-full
closed
1 week ago
1
Fixed render_r1_r2 function(s) in Snakefiles
#413
b-full
closed
1 week ago
0
Move strandednes in params
#412
b-full
closed
1 week ago
1
Fix unused r1_only parameter
#411
b-full
closed
2 weeks ago
1
Fix unused r1_only parameter
#410
b-full
closed
2 weeks ago
0
use fasterq-dump
#409
daler
opened
2 weeks ago
0
SRA runs should save data elsewhere and then symlink
#408
daler
opened
2 weeks ago
0
Layout rather than LibraryLayout
#407
daler
opened
2 weeks ago
2
r1_only=False
#406
daler
closed
1 week ago
1
move strandedness in params
#405
daler
opened
2 weeks ago
0
fix typo in clone command
#404
daler
closed
2 weeks ago
0
Fix R tests
#403
daler
closed
4 months ago
0
added Error documentation section to rnaseq-rmd.rst and hyperlnked to it in helpers.R error message
#402
menoldmt
opened
4 months ago
0
Limit background genes in overrepresentation analysis in functional-enrichment.Rmd
#401
Mira0507
closed
5 months ago
3
Adding universe to functional enrichment analysis
#400
Mira0507
closed
5 months ago
1
Generate RDS object ready for carnation
#399
mitraak
closed
5 months ago
1
V1.11
#398
daler
closed
1 month ago
0
add samtools stats and samtools flagstat
#397
daler
closed
5 months ago
0
Implemented LRT functionality
#396
menoldmt
closed
3 months ago
3
Add hyperlink to rnaseq.Rmd error message, 'duplicate names found after removing pattern ^contr_[^_]+_'
#395
menoldmt
opened
11 months ago
1
Added Error header in rnaseq-rmd.rst and docs for 'Found duplicate na…
#394
menoldmt
closed
4 months ago
0
Add documentation for "Found duplicate names after removing pattern ^contr_[^_]+_" error
#393
menoldmt
closed
11 months ago
0
Avoid overwriting combined.Rds in functional-enrichment.Rmd and gene-patterns.Rmd
#392
menoldmt
closed
1 week ago
2
In functional-enrichment.Rmd and gene-patterns.Rmd, add config for turning on/off lazy caching
#391
menoldmt
opened
1 year ago
1
Automatic plot resizing in gene-patterns
#390
menoldmt
opened
1 year ago
0
Add Functional Enrichment TSV Links to functional-enrichment.Rmd
#389
menoldmt
opened
1 year ago
0
Typographical errors in Gene-Patterns Explanatory Text
#388
menoldmt
opened
1 year ago
0
In gene-patterns.Rmd, ensure factors for certain colData used in gene patterns
#387
menoldmt
opened
1 year ago
0
PDF plots in gene-patterns.Rmd
#386
menoldmt
opened
1 year ago
0
Work in progress: CircleCI inline orbs
#385
aliciaaevans
opened
1 year ago
0
378 deploy script error
#384
aliciaaevans
closed
1 year ago
2
V1.10.3rc
#383
daler
closed
1 year ago
0
Update Snakefile - add `--countReadPairs` for PE featureCounts
#382
therealgenna
closed
1 year ago
0
consider using black/greylists for peak-calling
#381
daler
opened
1 year ago
0
Epic2
#380
Mira0507
closed
1 year ago
3
Epic2 peakcaller added to chipseq
#379
Mira0507
closed
1 year ago
0
Deploy script error
#378
njohnso6
closed
1 week ago
1
Adding Epic2 as a new peakcaller in chipseq
#377
Mira0507
closed
1 year ago
1
V1.10.2rc
#376
daler
closed
1 year ago
0
update multiqc configs
#375
daler
closed
1 year ago
0
Fix multiqc_config.yaml
#374
therealgenna
closed
1 year ago
1
copying vc docs rst
#373
fridells51
opened
1 year ago
0
pin cutadapt and python to help solving
#372
daler
closed
1 year ago
0
variant calling workflow + testing
#371
fridells51
opened
1 year ago
0
V1.10.1rc
#370
daler
closed
1 year ago
0
Check featurecounts & sampletable sample names in dds construction when subset_counts is not provided
#369
kcampbell824
closed
1 week ago
2
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