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vanheeringen-lab
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seq2science
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
https://vanheeringen-lab.github.io/seq2science
MIT License
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todo
#926
Rebecza
closed
1 year ago
2
samples and config cleanup
#925
Maarten-vd-Sande
closed
1 year ago
1
FR: single cell RNA filtering
#924
Maarten-vd-Sande
opened
1 year ago
0
BUG: qc_scRNA rules dont use params, so rerunning doesn't work
#923
Maarten-vd-Sande
opened
1 year ago
0
FR: single cell auto detection if droplet or cell based barcodes?
#922
Maarten-vd-Sande
closed
1 year ago
0
FR: python/scanpy interoperability for single cell?
#921
Maarten-vd-Sande
closed
1 year ago
0
Control sample added to trackhub
#920
Maarten-vd-Sande
closed
1 year ago
0
Update multiqc
#919
Maarten-vd-Sande
closed
1 year ago
0
update snakemake
#918
Maarten-vd-Sande
closed
1 year ago
0
Update kallistobus.yaml
#917
Maarten-vd-Sande
closed
1 year ago
1
height is specifyable
#916
Maarten-vd-Sande
closed
1 year ago
0
FR: cleanup for manuscript
#915
Maarten-vd-Sande
opened
1 year ago
0
reduce workflow image sizes
#914
siebrenf
closed
1 year ago
0
pretty docs DAGs
#913
siebrenf
closed
1 year ago
1
Update config.yaml
#912
Maarten-vd-Sande
closed
1 year ago
0
delete fastq files after downloading
#911
Maarten-vd-Sande
closed
1 year ago
0
updated scRNA yamls
#910
siebrenf
closed
1 year ago
0
fix docs environment
#909
Maarten-vd-Sande
closed
1 year ago
1
matplotlib fixed
#908
Maarten-vd-Sande
closed
1 year ago
0
BUG: [The new version of `matplotlib` will lead to some bugs in some rules.]
#907
bioqxu
closed
1 year ago
3
conda-forge > bioconda
#906
siebrenf
closed
1 year ago
0
BUG: plotfingerprint has no configurable options
#905
Maarten-vd-Sande
closed
1 year ago
0
Automate mitochondrial gene retrieval for SCTK QC
#904
tilschaef
opened
1 year ago
2
Fixes #900
#903
Maarten-vd-Sande
closed
1 year ago
1
BUG: Bigwig files not transferred to trackhub folder
#902
jroubroeks
closed
1 year ago
1
Update configuration_workflows.smk
#901
Maarten-vd-Sande
closed
1 year ago
0
UnboundLocalError: local variable 'kmer_size' referenced before assignment
#900
ivanferrreira
closed
1 year ago
19
Update util.py
#899
siebrenf
closed
1 year ago
0
Update deeptools.yaml
#898
siebrenf
closed
2 years ago
2
Update qc.smk
#897
Maarten-vd-Sande
closed
1 year ago
4
Update trackhub.smk
#896
siebrenf
closed
2 years ago
1
Config fix
#895
tilschaef
closed
2 years ago
0
BUG: sc post-processing currently not functional
#894
tilschaef
closed
2 years ago
1
Update kallistobus.yaml
#893
tilschaef
closed
2 years ago
0
fix ena urls
#892
Maarten-vd-Sande
closed
2 years ago
1
no multiqc files injection
#891
Maarten-vd-Sande
closed
2 years ago
0
Snakemake slight downgrade
#890
Maarten-vd-Sande
closed
2 years ago
0
BUG: barcode concatination scATAC
#889
JGASmits
closed
2 years ago
6
Update configuration_explain.smk
#888
Maarten-vd-Sande
closed
2 years ago
4
BUG: database disk image is malformed
#887
Maarten-vd-Sande
closed
2 years ago
0
BUG: softmask_track_1 gets stuck
#886
siebrenf
closed
1 year ago
1
update gimme
#885
siebrenf
closed
2 years ago
1
Update qc.smk
#884
Maarten-vd-Sande
closed
1 year ago
1
sralite downloads
#883
Maarten-vd-Sande
closed
2 years ago
1
fix #879, trackhub index
#882
Maarten-vd-Sande
closed
2 years ago
0
BUG: prefetch sometimes downloads .sralite files instead .sra
#881
Maarten-vd-Sande
closed
2 years ago
0
add niceness
#880
Maarten-vd-Sande
closed
2 years ago
1
BUG: trackhub index fails on BraLan3
#879
Maarten-vd-Sande
closed
2 years ago
4
Update requirements.yaml
#878
siebrenf
closed
2 years ago
2
samples in the cloud fix
#877
Maarten-vd-Sande
closed
2 years ago
0
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