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dib-lab
/
elvers
(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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binderizing eelpond
#113
ctb
opened
5 years ago
1
provide "getting started" tutorials for assembly/annotation AND for diffexp AND for both
#112
ctb
opened
5 years ago
0
update documentation on samples.tsv
#111
ctb
opened
5 years ago
1
meta issue for high-level error checking
#110
ctb
opened
5 years ago
2
single ended quantify/diffexp doesn't work.
#109
ctb
closed
5 years ago
8
[MRG] add a yeast differential expression example
#108
ctb
closed
5 years ago
7
unclear errors when config yaml file is badly formatted
#107
ctb
opened
5 years ago
1
`assemblyinput` should be `transcriptome` or `reference`
#106
ctb
closed
5 years ago
0
allow downloading of assembly?
#105
ctb
closed
5 years ago
1
untab comments in .yml files
#104
ctb
closed
5 years ago
0
running diffexp on examples/nema.yaml doesn't do anything?
#103
ctb
opened
5 years ago
3
[WIP] Documentation updates to make a strong initial user impression!
#102
ctb
opened
5 years ago
0
fix se trim param
#101
bluegenes
closed
5 years ago
1
[MRG] add multiqc rule
#100
bluegenes
closed
5 years ago
5
[MRG] Add rule testing framework
#99
bluegenes
closed
5 years ago
8
confusing lack of an error error when gene_trans_map is missing?
#98
ctb
closed
5 years ago
0
[WIP] newer deseq2
#97
bluegenes
closed
5 years ago
3
fix assemblyinput for ppl specifying out_path
#96
bluegenes
closed
5 years ago
1
[MRG] dont write report for create_envs_only
#95
bluegenes
closed
5 years ago
0
update deseq2 version
#94
bluegenes
opened
5 years ago
0
[MRG] override deseq2 default contrasts
#93
bluegenes
closed
5 years ago
1
better experiment param handling
#92
bluegenes
closed
5 years ago
0
fix out_path specification
#91
bluegenes
closed
5 years ago
0
Missing input files for rule deseq2_init_tx2gene
#90
johnsolk
closed
5 years ago
3
Could not create conda environment from dammit-env.yaml and deseq2-env.yaml
#89
johnsolk
closed
5 years ago
7
busco pipebricks issue
#88
bluegenes
opened
5 years ago
0
dammit install issue from db_extra flag/update docs
#87
ACharbonneau
closed
5 years ago
0
read table -> read csv
#86
bluegenes
closed
5 years ago
0
Trinity failing, empty log file
#85
mandyfrazier
opened
5 years ago
2
documentation improvements
#84
bluegenes
closed
5 years ago
1
read_table future warning
#83
ACharbonneau
closed
5 years ago
1
do not require samples tsv for assembly-based workflows
#82
bluegenes
closed
5 years ago
1
Explanation for my-samples.tsv headers?
#81
ACharbonneau
closed
5 years ago
1
typo and broken links in readme
#80
mandyfrazier
closed
5 years ago
2
how should we generate the gene to transcript map?
#79
ctb
opened
5 years ago
6
dammit step fails after rerunning assembly
#78
ctb
opened
5 years ago
1
if I remove the `assembly/` output directory, shouldn't eelpond rerun everything after that too?
#77
ctb
opened
5 years ago
2
is busco completeness output available anywhere?
#76
ctb
opened
5 years ago
2
Add eelpond tests/ directory
#75
charlesreid1
closed
5 years ago
2
combine units prior to khmer
#74
bluegenes
opened
5 years ago
8
Further improvements to DAG handling
#73
charlesreid1
closed
5 years ago
5
[MRG] fix URLs for nema example data
#72
ctb
closed
5 years ago
0
does diffexp include deseq2?
#71
ctb
closed
5 years ago
1
Fix typo in deseq2 doc
#70
ctb
closed
5 years ago
1
[MRG] Better dag handling
#69
bluegenes
closed
5 years ago
6
[MRG] fix pear
#68
bluegenes
closed
5 years ago
1
add sunbeam reference
#67
ctb
opened
5 years ago
0
what happens when you run eelpond from another directory?
#66
ctb
closed
5 years ago
0
add multiqc into eelpond preprocess workflow
#65
ctb
closed
5 years ago
1
write params file to output directory to track parameters used in an analysis
#64
ctb
opened
5 years ago
0
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