single-cell-genetics vireo issues

single-cell-genetics / vireo

Demultiplexing pooled scRNA-seq data with or without genotype reference

https://vireoSNP.readthedocs.io

Apache License 2.0

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issues

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GitHub shows 0.2.3 as latest release

#60 paulmenzel closed 2 years ago
2
Strategies for validating output

#47 hongdavid94 opened 2 years ago
4
vireo error with scipy.special.binom

#46 hongdavid94 closed 2 years ago
2
Subsetting a vcf file

#45 WWolf opened 2 years ago
1
Which VCF files to use for SNP calling?

#44 ShouWenWang opened 2 years ago
1
vireo and large dataset

#43 HibaLaghrissi opened 2 years ago
1
Vireo taking ages to run

#42 lucygarner opened 2 years ago
4
assignments between snRNA and snATAC

#41 Parul-Kudtarkar opened 2 years ago
3
Question: Bulk RNA-seq from nanopore?

#40 alexandruioanvoda opened 2 years ago
1
Vireo without Genotype (N=3) - high unassigned cells

#39 Parul-Kudtarkar opened 2 years ago
2
Clarifying the workflow using bulk RNA-seq data for genotyping

#38 lucygarner opened 2 years ago
1
all unassigned for 10x single cell RNAseq dataset using 1000genome vcf

#37 songeric1107 opened 2 years ago
3
Vireo misassigns cells to wrong donor.

#36 maxozo closed 2 years ago
3
Demultiplexing pooled samples w/o genotype (dialing number of samples)

#35 Parul-Kudtarkar closed 2 years ago
3
combine multiple donor vcf

#33 AnjaliC4 opened 2 years ago
8
Does running Vireo in linux without a genotype file require the sparse matrix to be in vcf format?

#32 alexisweber opened 2 years ago
1
cellSNP-lite incompatibility

#31 drneavin closed 2 years ago
3
High amount of cells that remain unassigned and differing results

#30 mihem closed 3 years ago
3
identify contaminant population

#29 bobermayer closed 3 years ago
6
Uninformative MemoryError message

#28 Zepeng-Mu opened 3 years ago
5
snATAC implimentation

#27 kvshams closed 3 years ago
1
option cell_file not defined

#26 Zepeng-Mu closed 3 years ago
1
Large number of `doublet` and `unassigned`, most lost from specific donor(s), after removing doublets

#25 PeteHaitch opened 3 years ago
6
high unassigned in 10x single nucleus RNA seq

#24 evolanna opened 3 years ago
1
Please help me pinpoint cause of high unassigned/doublets

#23 mperalc closed 3 years ago
7
ImportError..... failed to map segment from shared object: Cannot allocate memory

#22 maojn opened 3 years ago
1
cann't finish the step of plotting fig_GT_distance

#21 plrlhb12 closed 3 years ago
4
Fixed error in output with --noDoublet & slice cells

#20 cziegenhain closed 3 years ago
2
snATAC-seq?

#19 HaglundA closed 4 years ago
1
Different result with same file and cmd

#18 mengchengyao opened 4 years ago
2
Recovering donor identity in known genotype mode

#17 vals closed 4 years ago
3
Create mitoMut.py

#16 aaronkwc closed 4 years ago
0
wrapper function for mito mut

#15 aaronkwc closed 4 years ago
0
Recommended tools for bulk RNA-seq genotyping for mode 2

#14 lmweber closed 4 years ago
2
Vireo with both known and unknown genotypes in sample

#13 bio-la closed 4 years ago
2
using Vireo for celseq2 data

#12 dwkarjosukarso closed 3 years ago
3
[vireo] IndexError: too many indices for array

#11 luzgaral closed 3 years ago
1
Bug fixes when reading VCF file

#10 andr-kun closed 4 years ago
1
Vireo object-oriented implementation

#9 huangyh09 closed 4 years ago
0
Vireo new mode for variant specific ASE

#8 huangyh09 closed 4 years ago
0
Output genotype data with vartrix files

#7 GWW closed 4 years ago
4
update ASE branch from master branch

#6 huangyh09 closed 4 years ago
0
Error when using --forceLearGT

#5 drneavin opened 5 years ago
0
Error When Writing out GT_donors.vcf

#4 drneavin closed 5 years ago
8
error when loading donor VCF

#3 slyahn closed 5 years ago
3
Providing multiple VCFs to vireo

#2 onecarbon closed 3 years ago
5
Genotype strategy

#1 coh-racng closed 5 years ago
1