cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data (by single-cell-genetics)
cellsnp-lite
Efficient genotyping bi-allelic SNPs on single cells (by single-cell-genetics)
| cellSNP | cellsnp-lite | |
|---|---|---|
| 2 | 1 | |
| 69 | 117 | |
| - | 2.6% | |
| 0.0 | 7.1 | |
| almost 2 years ago | 24 days ago | |
| Python | C | |
| Apache License 2.0 | Apache License 2.0 |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
cellSNP
Posts with mentions or reviews of cellSNP.
We have used some of these posts to build our list of alternatives
and similar projects.
-
How to create VCFs for scRNA-Seq data sets
cellSNP is popular and works well.
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Annotating variants in single-cell sequencing data
The authors of vireo have a tool called cellSNP that may be helpful as well.
cellsnp-lite
Posts with mentions or reviews of cellsnp-lite.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-03-20.
-
Genotype single cell data?
Commenting in case anyone else needs a solution: cellSNP-lite took in the bam files and generated variant calls. Can be used with or without a list of SNPs for comparisons, RNA, ATAC, bulk or single cell!
What are some alternatives?
When comparing cellSNP and cellsnp-lite you can also consider the following projects:
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
awesome-single-cell - Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
COVID-19-RNA-Seq-datasets - A repository for sharing information on available COVID-19 RNA-Seq datasets
popscle - A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools