rnaseqc
Fast, efficient RNA-Seq metrics for quality control and process optimization (by getzlab)
popscle
A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools (by statgen)
| rnaseqc | popscle | |
|---|---|---|
| 1 | 1 | |
| 141 | 43 | |
| 0.7% | - | |
| 4.5 | 2.7 | |
| about 2 months ago | about 3 years ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | 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.
rnaseqc
Posts with mentions or reviews of rnaseqc.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-10-08.
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Tools for strand direction detection RNA-Seq
I like to use RNA-SeQC (https://github.com/getzlab/rnaseqc). It shows the percentage of forward/reverse reads that alingned to either the sense or antisense strands. It is also compatible with multiQC which is a big plus.
popscle
Posts with mentions or reviews of popscle.
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?
You can get vcf files from 10x bam files with freemuxlet. ATAC-seq or RNA-seq.
What are some alternatives?
When comparing rnaseqc and popscle you can also consider the following projects:
rnaseq - RNA-seq analyses.
scCODA - A Bayesian model for compositional single-cell data analysis
salmon - 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
cellsnp-lite - Efficient genotyping bi-allelic SNPs on single cells
TPMCalculator - TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files
seurat - R toolkit for single cell genomics
how_are_we_stranded_here - Check strandedness of RNA-Seq fastq files