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

71 stars 27 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Check if cell data has any variant and check if cell data variants ha…

#108 ghuls opened 1 week ago
0
updated release for 0.5.8

#107 chouellaine opened 1 month ago
1
Why those cells are unassigned?

#106 tewengtong opened 2 months ago
3
VCFfiles: seperated or merged

#105 hsymoon opened 2 months ago
2
ValueError: column index exceeds matrix dimensions

#104 hsymoon opened 2 months ago
3
Extracting cell barcodes

#103 emmascne closed 2 months ago
0
Error: require the same format for all variants.

#102 hsymoon opened 3 months ago
1
Handling Multiple Sequencing Lanes and Donor Information in VireoSNP

#101 sxf-ux closed 3 months ago
1
vcf file for GTbarcode output

#100 Sharm8 closed 4 months ago
2
Most cells are unassigned and a few of them do not match the filters

#99 txemaheredia opened 5 months ago
7
Low doublet detection rate

#98 DHelix closed 5 months ago
1
questions about the output

#97 Sharm8 closed 4 months ago
0
A large number of cells are unassigned & very few n_vars

#96 nansne opened 6 months ago
3
Demultiplexing multiomic sequencing data

#95 DHelix opened 6 months ago
2
Export cell-level variant calls?

#94 bbimber closed 6 months ago
1
ELBO metric when running vireo from the command line?

#93 jamesnemesh opened 6 months ago
0
Discriminative variants with GTbarcode

#92 flde opened 6 months ago
4
Using Simulate to make distinct barcodes

#91 Sun-storm closed 7 months ago
3
Feature/allow empty vcfs

#90 njbernstein closed 7 months ago
0
Beneficial to pool .bam files from seperate 10x single-cell lanes instead of demultilplexing seperately?

#89 koefoeden opened 10 months ago
7
ForceLearnGT leads to very different result

#88 mihem closed 11 months ago
10
Inferring consensus genotype for N=1

#87 Ngort opened 1 year ago
0
Add all used FORMAT tags when writing VCF files.

#86 ghuls closed 7 months ago
2
Subsetting donor VCF file for Vireo strategy 2

#85 lucygarner opened 1 year ago
3
ValueError: could not convert string to float: '.'

#84 algarnham opened 1 year ago
1
Error when running vireo mode 2 with option -N 1

#83 calebthomas259 opened 1 year ago
1
Questions about filtering SNPs in donor VCF file

#82 calebthomas259 closed 1 year ago
2
Version less memory intensive and better MT handling + merge bams w/o vcf

#81 clementhelsens closed 7 months ago
2
How to export the cell barcodes for each clone identified

#80 haigdjambazian opened 1 year ago
5
Does vireo catch both hetero- and homo-zygous doublets?

#79 ollieeknight closed 1 year ago
1
Unclear Usage for CITE-seq Data

#78 DarioS opened 1 year ago
0
Use Manual Lacks Information About Output Files

#77 DarioS opened 1 year ago
1
TypeError: cannot unpack non-iterable NoneType object

#76 padro89 opened 1 year ago
6
TypeError: '>=' not supported between instances of 'NoneType' and 'int'

#75 alexisweber opened 1 year ago
1
IndexError: index (875606) out of range

#74 maxozo closed 1 year ago
2
flag -v --version

#73 edgano closed 1 year ago
1
Using Sample Genotypes

#72 alexisweber closed 1 year ago
1
Guidance to verify paired samples from the same donor: do we need to merge bam files?

#71 wilfridricher closed 1 year ago
1
10x Multiome RNA vs ATAC data from same cells confidently disagrees on donor identities

#70 koefoeden opened 2 years ago
9
Assign donor ids to actual donor

#69 Parul-Kudtarkar opened 2 years ago
2
-N flag behavior

#68 racng closed 2 years ago
1
vireo detects 0 variants

#67 DanielMedinaCano opened 2 years ago
0
Cells unassigned by using snp array

#66 yilevine opened 2 years ago
4
Memory overload for large number of patients

#65 racng opened 2 years ago
3
All cells unassigned in 10x snRNA-seq data

#64 ninasachdev opened 2 years ago
3
Multiome data demultiplexing

#63 zhijunyuu closed 2 years ago
4
Genotyping with information of recepient

#62 flde closed 2 years ago
5
Proper steps for cellSNP and Vireo for large dataset

#61 vincycheng opened 2 years ago
4
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