clustifyr
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets (by rnabioco)
rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth. (by snakemake-workflows)
clustifyr | rna-seq-kallisto-sleuth | |
---|---|---|
1 | 1 | |
101 | 63 | |
0.0% | - | |
4.9 | 5.9 | |
23 days ago | 21 days ago | |
R | Python | |
MIT License | MIT License |
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.
clustifyr
Posts with mentions or reviews of clustifyr.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Compare specific clusters across condition in scRNA-seq
You can use the package clustifyr in r with seurat and use a known data set that has already been identified. It will give you a correlation matrix to define how close your “unknown” cluster is to a already identified cluster. However this all depends on if you have a good reference data set clustifyr
rna-seq-kallisto-sleuth
Posts with mentions or reviews of rna-seq-kallisto-sleuth.
We have used some of these posts to build our list of alternatives
and similar projects.
-
qiime2 but for RNAseq data?
(repo is here: https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth)
What are some alternatives?
When comparing clustifyr and rna-seq-kallisto-sleuth you can also consider the following projects:
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
drake - An R-focused pipeline toolkit for reproducibility and high-performance computing
biomisc_R - command line bioinformatic scripts written in R
reprex - Render bits of R code for sharing, e.g., on GitHub or StackOverflow.
targets - Function-oriented Make-like declarative workflows for R
wiggleplotr - A small R package to make sequencing read coverage plots in R.
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data