rna-seq-kallisto-sleuth
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth. (by snakemake-workflows)
wiggleplotr
A small R package to make sequencing read coverage plots in R. (by kauralasoo)
| rna-seq-kallisto-sleuth | wiggleplotr | |
|---|---|---|
| 1 | 1 | |
| 63 | 33 | |
| - | - | |
| 5.9 | 10.0 | |
| 20 days ago | almost 2 years ago | |
| Python | R | |
| 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.
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)
wiggleplotr
Posts with mentions or reviews of wiggleplotr.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-03-03.
-
representing gene/transcript layout with variants, suitable approaches?
https://github.com/dzhang32/ggtranscript and https://github.com/kauralasoo/wiggleplotr look like good starting points, and since they output ggplot objects you can add some layers (like geom_segment or other geometries, and ggrepel for labels) to annotate them. Otherwise you can go the "from scratch" route using ggplot with some polygons and segments.
What are some alternatives?
When comparing rna-seq-kallisto-sleuth and wiggleplotr you can also consider the following projects:
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
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
hecatomb - hecatomb is a virome analysis pipeline for analysis of Illumina sequence data