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theislab
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hadge
Comprehensive pipeline for donor demultiplexing in single cell
https://hadge.readthedocs.io/en/latest/
MIT License
24
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6
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Fixes to Hashing side
#59
mari-ga
opened
2 months ago
0
Unable to pip install PyVCF
#58
JHYSiu
opened
4 months ago
1
Souporcell clustering panicked at 'no entry found for key' for some samples
#57
bednarsky
opened
4 months ago
0
hashing demultiplexing pipeline errors
#56
michaelplynch
opened
4 months ago
1
Fix freebayes parameter
#55
wxicu
closed
5 months ago
0
elaboration on sample vs donor
#54
julicudini
closed
5 months ago
2
souporcell_pipeline.py: command not found
#53
bednarsky
closed
5 months ago
5
add conda channels for samtools, scanpy, muon
#52
knollr
closed
6 months ago
1
samtools channel missing
#51
knollr
closed
6 months ago
1
freebayes could not parse maxComplexGap
#50
bednarsky
opened
6 months ago
2
Souporcell fails due to bcftools not found
#49
bednarsky
closed
5 months ago
3
nf-core modules
#48
Zethson
opened
8 months ago
0
Bring the pipeline to nf-core
#47
Zethson
opened
8 months ago
0
Missing conda recipes
#46
Zethson
opened
8 months ago
2
Improve documentation
#45
wxicu
closed
8 months ago
1
Error: HADGE:run_multi:gene_demultiplexing:variant_cellSNP:cellSNP (1): Not a valid path value: 'None'
#44
zimea
closed
6 months ago
8
Deconvolution with known SNPs per sample - vcf_donor vs vcf_mixed
#43
bednarsky
closed
6 months ago
3
running on multiple samples
#42
isadeghi87
closed
6 months ago
7
An attempt to run hadge with Singularity containers
#41
kauralasoo
opened
9 months ago
3
Merge from main
#40
wxicu
closed
9 months ago
0
improve description of inputs
#39
bio-la
opened
9 months ago
5
Issues with the containers for hash processing
#38
maxozo
opened
10 months ago
0
Some modifications made to Hadge that were esential for running large scale processing of Onek1k data
#37
maxozo
closed
9 months ago
0
Merge from main
#36
wxicu
closed
10 months ago
1
Improve docs
#35
wxicu
closed
10 months ago
0
Test should test all methods
#34
Zethson
opened
10 months ago
0
nf-core-ize notes
#33
edmundmiller
opened
1 year ago
1
Fix bug when no hto or rna matrix is provided for summary
#32
wxicu
closed
1 year ago
0
Error: run_multi:gene_demultiplexing:summary (1); work-dir=null: Not a valid path value: 'None'
#31
bednarsky
closed
10 months ago
2
Vireo error: _multiprocessing.cpython-39-x86_64-linux-gnu.so: failed to map segment from shared object
#30
bednarsky
opened
1 year ago
1
Add notebook to sphinx
#29
Zethson
closed
1 year ago
1
Render notebook
#28
Zethson
closed
1 year ago
0
Correction for old merge
#27
mari-ga
closed
10 months ago
0
Merging changes
#26
mari-ga
closed
1 year ago
0
Freemuxlet fails during popscle dsc-pileup due to different order of bam and vcf.
#25
bednarsky
closed
1 year ago
5
Add new profiles to hadge
#24
wxicu
closed
1 year ago
4
Error demuxlet: work-dir=null, Path value cannot be null
#23
bednarsky
closed
1 year ago
3
Potential variable name bug - freemuxlet.nf: grouplist_name
#22
bednarsky
closed
1 year ago
3
Restructure the docs
#21
wxicu
closed
1 year ago
1
Fixes for Multi-sample, implementation of MuData and Docs for hashing
#20
mari-ga
closed
1 year ago
2
Fix RTD
#19
Zethson
closed
1 year ago
0
update nextflow config
#18
wxicu
closed
1 year ago
0
Fix bug when not generating anndata
#17
wxicu
closed
1 year ago
0
update
#16
wxicu
closed
1 year ago
0
update doc for running multi-samples
#15
wxicu
closed
1 year ago
0
Fix bug of running multi-sample
#14
wxicu
closed
1 year ago
0
New tools implementation
#13
mari-ga
closed
1 year ago
3
fix some existing errors
#12
wxicu
closed
1 year ago
0
Enable running multi-samples
#11
wxicu
closed
1 year ago
0
Implementation of new tools
#10
mari-ga
closed
1 year ago
2
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