rhmmer
Simple R utilities for working with HMMER (by arendsee)
Baltica
Baltica: integrated differential junction usage (by dieterich-lab)
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.
rhmmer
Posts with mentions or reviews of rhmmer.
We have used some of these posts to build our list of alternatives
and similar projects.
-
how to work with a hmmsearch table output?
I use this R package in Rstudio; https://github.com/arendsee/rhmmer
Baltica
Posts with mentions or reviews of Baltica.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Novel Splice Variants in RNAseq Data
Also, we've been working on a framework with multiple workflows for differential splicing: Baltica: integrated differential junction usage (DJU) https://github.com/dieterich-lab/Baltica . Please have on mind that Baltica is work in progress, but the workflows are quite mature. Fell free to contact me if you have any questions!
What are some alternatives?
When comparing rhmmer and Baltica you can also consider the following projects:
heatitup
awesome-single-cell - Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
biomisc_R - command line bioinformatic scripts written in R
drugfindR - Repository holding the code for the drugfindR R package
maftools - Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
ermineR - R wrapper for ermineJ
bio-sequence
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package