diffexpr
Porting DESeq2 into python via rpy2 (by wckdouglas)
cellSNP
Pileup biallelic SNPs from single-cell and bulk RNA-seq data (by single-cell-genetics)
| diffexpr | cellSNP | |
|---|---|---|
| 1 | 2 | |
| 68 | 69 | |
| - | - | |
| 2.7 | 0.0 | |
| 11 months ago | almost 2 years ago | |
| Python | Python | |
| MIT License | 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.
diffexpr
Posts with mentions or reviews of diffexpr.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-02-23.
-
Introduction to RNAseq and microRNA?
I was able to run deseq2 in Python with this wrapper: https://github.com/wckdouglas/diffexpr
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.
-
Annotating variants in single-cell sequencing data
The authors of vireo have a tool called cellSNP that may be helpful as well.
What are some alternatives?
When comparing diffexpr and cellSNP you can also consider the following projects:
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Vcflib - C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
PyDESeq2 - A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
COVID-19-RNA-Seq-datasets - A repository for sharing information on available COVID-19 RNA-Seq datasets
cellsnp-lite - Efficient genotyping bi-allelic SNPs on single cells