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imbforge
/
NGSpipe2go
a set of NGS pipelines
GNU General Public License v3.0
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10
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Tool Version Updates & Minor Fixes
#69
chdietrich
closed
6 months ago
1
Dead links
#68
adomingues
closed
2 years ago
0
aggregated multi-sample FastQC plots
#67
ssayols
closed
2 years ago
0
shinyreports.vars.groovy should not have *any* hardcoded directory
#66
ssayols
closed
2 years ago
0
[most] modules' vars map should have outdir and logdir
#65
ssayols
closed
2 years ago
0
identification string for all pipelines
#64
ssayols
closed
5 years ago
0
use \${TMP} to sort bam file
#63
ssayols
closed
2 years ago
1
new module to collect tool versions
#62
ssayols
closed
2 years ago
0
module exit strings
#61
ssayols
closed
2 years ago
0
add test dataset for scRNA-seq
#60
ssayols
closed
2 years ago
1
add smallRNA-seq test dataset
#59
ssayols
closed
5 years ago
1
add test dataset for rna-seq paired end
#58
ssayols
closed
2 years ago
0
add test dataset for chip-seq paired end
#57
ssayols
closed
2 years ago
0
Make "standard" miRNA and piRNA pipelines from the smallRNA-seq pipelines
#56
ssayols
closed
2 years ago
0
adapt SmallRNA-seq (BCF) pipeline to the new architecture
#55
ssayols
closed
5 years ago
1
adapt scRNA-seq pipeline to the new architecure
#54
ssayols
closed
5 years ago
1
adapt rna-seq variant calling pipeline to the new architecure
#53
ssayols
closed
5 years ago
1
adapt dna-seq pipeline to the new architecure
#52
ssayols
closed
5 years ago
1
adapt rna-seq pipeline to the new architecture
#51
ssayols
closed
5 years ago
1
adapt chip-seq pipeline to the new architecture
#50
ssayols
closed
5 years ago
1
New DNA methylation pipeline
#49
ssayols
closed
2 years ago
0
MultiQC NGS module
#48
ssayols
closed
5 years ago
3
ChIP-seq pipeline - longnames
#47
adomingues
closed
5 years ago
0
Stages to filter alignments
#46
adomingues
closed
5 years ago
0
Add legend to gene body coverage plots
#45
adomingues
closed
5 years ago
0
DESeq2: output Dispersion plot
#44
adomingues
closed
5 years ago
1
Sample correlation
#43
adomingues
closed
5 years ago
0
Unavailable R version
#42
adomingues
closed
7 years ago
0
bowtie1pe and fastq.gz
#41
adomingues
closed
7 years ago
2
Cutadapt plots are not representing true values
#40
adomingues
closed
5 years ago
0
Slurm --> master
#39
ssayols
closed
7 years ago
0
Style guide
#38
adomingues
closed
6 years ago
3
Slurm transition
#37
adomingues
closed
7 years ago
1
use function parameters and return values
#36
oliverdrechsel
closed
5 years ago
1
MultiQC like plots
#35
oliverdrechsel
closed
5 years ago
0
env.sh requirement
#34
AMChalkie
closed
6 years ago
1
DE analysis report: show 2 FDR thresholds (text + MA + volcano)
#33
ssayols
closed
5 years ago
0
make multimappers venn smaller in the report
#32
ssayols
closed
6 years ago
1
split markduplicates module into mark+remove
#31
ssayols
closed
6 years ago
0
improve the ChIPseq report
#30
karaulanov
closed
5 years ago
1
samtools & picard should source env.sh as well
#29
oliverdrechsel
closed
8 years ago
0
Samtools with env.sh
#28
nkreim
closed
8 years ago
0
Add TOOL_JAVA var to control for the java version
#27
ssayols
closed
8 years ago
0
Merging the 2 forks
#26
adomingues
closed
8 years ago
0
Remove duplicates: switch from Picard to bamUtil
#25
oliverdrechsel
closed
8 years ago
1
shiny.helpers - full roxygen documentation of functions
#24
oliverdrechsel
closed
5 years ago
0
improve the text of the report
#23
oliverdrechsel
closed
8 years ago
0
identify test data set (the from csaw paper?)
#22
oliverdrechsel
closed
6 years ago
2
add venn diagram with peaks called per replicate (ranges)
#21
oliverdrechsel
closed
8 years ago
1
add motif discovery (rGadem)
#20
oliverdrechsel
closed
5 years ago
0
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