diffexpr
rna-seq-kallisto-sleuth
| diffexpr | rna-seq-kallisto-sleuth | |
|---|---|---|
| 1 | 1 | |
| 68 | 63 | |
| - | - | |
| 2.7 | 5.9 | |
| 11 months ago | 9 days ago | |
| Python | Python | |
| MIT License | MIT License |
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diffexpr
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Introduction to RNAseq and microRNA?
I was able to run deseq2 in Python with this wrapper: https://github.com/wckdouglas/diffexpr
rna-seq-kallisto-sleuth
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qiime2 but for RNAseq data?
(repo is here: https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth)
What are some alternatives?
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
PyDESeq2 - A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
clustifyr - Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
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