ermineR
R wrapper for ermineJ (by PavlidisLab)
rhmmer
Simple R utilities for working with HMMER (by arendsee)
ermineR | rhmmer | |
---|---|---|
1 | 1 | |
6 | 14 | |
- | - | |
0.0 | 0.0 | |
over 1 year ago | over 1 year ago | |
R | R | |
GNU General Public License v3.0 or later | 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.
ermineR
Posts with mentions or reviews of ermineR.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Gene ontology of differentially expressed genes in R
I would recommend ermineJ as thier statistical approach is better suited to overcome issues with how GO is constructed and the imbalance in the sizes of GO terms (sizes meaning the number of genes assigned). They have a graphical, command line interface and an R package link
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
What are some alternatives?
When comparing ermineR and rhmmer you can also consider the following projects:
full_spectrum_bioinformatics - An open-access bioinformatics text
Baltica - Baltica: integrated differential junction usage
heatitup
orthologr - Genome wide orthology inference and dNdS estimation
biomisc_R - command line bioinformatic scripts written in R
maftools - Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
bio-sequence
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package