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sequana
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rnaseq
RNA-seq, QC and differential analysis pipeline
BSD 3-Clause "New" or "Revised" License
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Update summary, pin sequana to use new plots
#47
cokelaer
closed
2 months ago
0
fix regressionm update pyproject
#46
cokelaer
closed
2 months ago
0
plot feature counts does not appear
#45
cokelaer
closed
2 months ago
0
Fix the default rRNA
#44
cokelaer
closed
8 months ago
1
consider splitting the HTML page into 1 page per comparison
#43
cokelaer
opened
9 months ago
0
rRNA is set to empty string (regression)
#42
cokelaer
closed
8 months ago
0
Fix typo for multiqc bowtie2 paired reports
#41
cokelaer
closed
10 months ago
0
change aligner -> aligner_choice to be sequanix comptabible
#40
cokelaer
closed
8 months ago
0
Fix bowtie1 regression (log).
#39
cokelaer
closed
10 months ago
1
add rnaseqc container and update rseqc
#38
cokelaer
closed
10 months ago
1
Refactorisation to use click
#37
cokelaer
closed
10 months ago
0
Document the sequana rnadiff standalone including the rtools container
#36
cokelaer
opened
1 year ago
0
Fix Annotation plot, add new expression plot
#35
cokelaer
closed
1 year ago
0
plot showing most expressed genes
#34
cokelaer
closed
1 year ago
1
fastp multiqc shows only 1 sample
#33
cokelaer
closed
1 year ago
1
Fixes #31 and #15
#32
cokelaer
closed
1 year ago
0
add option to not perform rRNA
#31
cokelaer
closed
1 year ago
0
Fix options not used in star_mapping
#30
cokelaer
closed
1 year ago
1
update new apptainer for graphviz
#29
cokelaer
closed
1 year ago
0
ashr required in new analysis. Need a new singularity
#28
cokelaer
closed
1 year ago
1
Fixing CI action (apptainer)
#27
cokelaer
closed
1 year ago
0
table in HTML reports limited to 20 comparisons
#26
cokelaer
closed
1 year ago
1
move containers in the config file
#25
cokelaer
closed
1 year ago
1
update workflow to use fastp wrapper
#24
cokelaer
closed
1 year ago
1
Improve output table csv file per comparison
#23
khourhin
opened
1 year ago
1
Fix python3.8 and 3.9 requirements
#22
cokelaer
closed
1 year ago
0
rnadiff directory should be cleaned from deset previous results when rerun with --force
#21
cokelaer
closed
1 year ago
1
remove upset plot if only one comparison is available
#20
cokelaer
closed
10 months ago
1
Fix strand balance automatic selection bug
#19
cokelaer
closed
2 years ago
1
config file not configure properly for sequanix
#18
cokelaer
closed
10 months ago
1
Update CI and switch branch from master to main
#17
cokelaer
closed
2 years ago
1
Fixing CI
#16
cokelaer
closed
2 years ago
0
pipeline does not work if fastp rule is deactivate
#15
ddesvillechabrol
closed
1 year ago
1
gene HTML tables are sometimes not appearing
#14
khourhin
closed
2 years ago
1
Update Readme to 0.15.1 (bowtie2 align wrapper update)
#13
khourhin
closed
2 years ago
1
Error in rnaseq.rules
#12
PierreL-B
closed
2 years ago
2
error in bowtie2_index.rules
#11
PierreL-B
closed
3 years ago
1
multiple feature counts
#10
cokelaer
closed
3 years ago
1
simplify start_mapping rule
#9
cokelaer
closed
3 years ago
1
seg fault star mapping
#8
cokelaer
closed
3 years ago
1
Error in indexing : do not create SAIndex output file
#7
PierreL-B
closed
3 years ago
2
large memory required in onsuccess when creating files from GFF file
#6
cokelaer
closed
3 years ago
1
tolerance argument in get_most_probable_strand_consensus() function
#5
PierreL-B
closed
3 years ago
1
pre-fill parameters related to indexing
#4
cokelaer
closed
4 years ago
1
explanation of the naming convention in the config and pipeline when using bowtie2_mapping rule
#3
cokelaer
closed
4 years ago
1
improvements rnaseq pipeline
#2
cokelaer
opened
4 years ago
0
simplify pipeline
#1
cokelaer
closed
4 years ago
1