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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Large number of unassigned

#110 Run2309 opened 1 week ago
0
Synthetic Bams -- High Disconcordance Rate

#109 marcus-tutert opened 1 month ago
0
Check if cell data has any variant and check if cell data variants ha…

#108 ghuls opened 2 months ago
0
updated release for 0.5.8

#107 chouellaine opened 3 months ago
1
Why those cells are unassigned?

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

#105 hsymoon opened 4 months ago
2
ValueError: column index exceeds matrix dimensions

#104 hsymoon opened 4 months ago
3
Extracting cell barcodes

#103 emmascne closed 4 months ago
0
Error: require the same format for all variants.

#102 hsymoon opened 5 months ago
1
Handling Multiple Sequencing Lanes and Donor Information in VireoSNP

#101 sxf-ux closed 5 months ago
1
vcf file for GTbarcode output

#100 Sharm8 closed 6 months ago
2
Most cells are unassigned and a few of them do not match the filters

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

#98 DHelix closed 7 months ago
1
questions about the output

#97 Sharm8 closed 6 months ago
0
A large number of cells are unassigned & very few n_vars

#96 nansne opened 7 months ago
3
Demultiplexing multiomic sequencing data

#95 DHelix opened 7 months ago
2
Export cell-level variant calls?

#94 bbimber closed 8 months ago
1
ELBO metric when running vireo from the command line?

#93 jamesnemesh opened 8 months ago
0
Discriminative variants with GTbarcode

#92 flde opened 8 months ago
4
Using Simulate to make distinct barcodes

#91 Sun-storm closed 8 months ago
3
Feature/allow empty vcfs

#90 njbernstein closed 9 months ago
0
Beneficial to pool .bam files from seperate 10x single-cell lanes instead of demultilplexing seperately?

#89 koefoeden opened 1 year ago
7
ForceLearnGT leads to very different result

#88 mihem closed 1 year 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 9 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 9 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
1
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 2 years 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