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single-cell-genetics
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cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells
https://cellsnp-lite.readthedocs.io
Apache License 2.0
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#129
Sun-storm
opened
1 week ago
5
update docs
#128
hxj5
closed
1 week ago
0
10X 5' single-cell data
#127
HenriettaHolze
opened
3 weeks ago
2
Multiple Samples Per Individual Query
#126
sxf-ux
closed
2 weeks ago
3
Generating Single VCF file for Each scRNA-Seq Sample
#125
hkarakurt8742
opened
4 weeks ago
3
Matching SNPs to cell barcode
#124
malonzm1
opened
1 month ago
0
Update docs and post-hoc analysis
#123
hxj5
closed
2 months ago
0
Combined max depth is above 1M. Potential memory hog! / Recommendations for maxDepth?
#122
bbimber
closed
3 months ago
2
UMI Collapsing
#121
grasshoffm
closed
3 months ago
5
Unable to install through anaconda
#120
Angelos-Gk
opened
3 months ago
8
Could not retrieve index file for .bam
#119
nansne
opened
3 months ago
3
Strand specificity
#118
flde
opened
3 months ago
1
[E::bgzf_flush] File write failed (wrong size)
#117
ghuls
closed
3 months ago
2
--help/--version should exit with status 0 (and write to stdout)
#116
jemma-nelson
closed
4 months ago
1
Integrating mouse SNPs and scRNA-seq data for imprinted gene identification
#115
singcell
opened
4 months ago
0
Converting cellsnp-lite outputs to vartrix's consensus matrix
#114
mdmanurung
opened
5 months ago
1
Is there a good way to identify and add the gene names to the output vcfs?
#113
pchatterjee7
opened
6 months ago
1
Manual: major update
#112
hxj5
closed
6 months ago
0
Use cellSNP on a big BAM file
#111
RosaDeSa
opened
7 months ago
1
improve documentation, fix readthedocs dependencies, initialize post-hoc analysis
#110
hxj5
closed
7 months ago
0
In a given SNP region, what are the criteria being used to categorize a cell as WT(0/0), heterozygote(1/0), and homozygote(1/1)?
#109
jiehuichen
closed
7 months ago
4
minimal minor allele count filter?
#108
chilampoon
closed
7 months ago
2
How to check the real reads cover an SNP in a cell?
#107
jiehuichen
closed
7 months ago
4
cellsnp-lite on data from 1 donor
#106
astaburuaga-garcia
opened
8 months ago
2
get unwanted allele in ALT column
#105
jiehuichen
closed
8 months ago
2
10x scATAC-seq like bam file, No reads captured with "--UMItag None"
#104
jiehuichen
closed
8 months ago
5
improve VCF header formatting
#103
hxj5
closed
10 months ago
0
the resulting file has only the title and no content
#102
suhuanhou
opened
10 months ago
6
Fix support for "--doubletGL" argument.
#101
ghuls
closed
10 months ago
4
scRNA-seq from different donors as a genotype-vcf input for vireo
#100
mariafiruleva
opened
10 months ago
6
Add a proper VCF header to "cellSNP.base.vcf.gz".
#99
ghuls
closed
11 months ago
0
-ldeflate is missing in Makefile after I executed ./configure
#98
darkcircle
opened
1 year ago
0
csp_utils: sort mtx by 1st column first
#97
hxj5
closed
1 year ago
0
postprocessing cellsnp outputs
#96
maxozo
opened
1 year ago
1
miscount alleles single-cell ATAC-seq
#95
raul-w
closed
1 year ago
4
Error when using more than 2 bam files with mode 1B
#94
cameronyoungpark
opened
1 year ago
5
OTH ratio 1
#93
flde
opened
1 year ago
5
add csp_utils for post-processing outputs
#92
hxj5
closed
1 year ago
0
Application to Slide-seq V2 returns empty vcf
#91
kzb193
closed
1 year ago
3
Filter SNPs by minMAF after running cellsnp-lite
#90
flde
closed
1 year ago
8
How to use cellsnp-lite
#89
DaliBAmor
closed
1 year ago
1
The 19 of 20 parallelized workers always strike far before the whole job is done
#88
mimi3421
opened
1 year ago
3
Handling haploid cells
#87
haigdjambazian
closed
1 year ago
2
Genotyping ATAC from WES vcf
#86
ollieeknight
closed
1 year ago
5
more reads filter options?
#85
zhentaoyoung
closed
1 year ago
4
hg38 chromsome names in 1000G VCF and 10X BAM
#84
jnktsj
closed
1 year ago
2
update to v1.2.3
#83
hxj5
closed
1 year ago
0
update manual
#82
hxj5
closed
1 year ago
0
Barcodes File Clarification
#81
DarioS
closed
1 year ago
3
Duplicate barcodes error?
#80
terencewtli
closed
1 year ago
2
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