rna-seq-kallisto-sleuth
biomisc_R
| rna-seq-kallisto-sleuth | biomisc_R | |
|---|---|---|
| 1 | 3 | |
| 63 | 23 | |
| - | - | |
| 5.9 | 0.0 | |
| 20 days ago | almost 2 years ago | |
| Python | R | |
| MIT License | MIT License |
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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)
biomisc_R
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Splitting multifast file into individual single fasta R
https://github.com/olgatsiouri1996/biomisc_R/blob/main/fasta_manipulation/split_multifasta_to_singlefasta.R this will help. I would recommend using sed to keep only the ids and not the full fasta headers
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how can I have R go through a fasta file opened with seqinr and run certain functions on each sequence?
https://github.com/olgatsiouri1996/biomisc_R/blob/main/sequence_statistics/calculate_biophysical_properties_multifasta.R this might help
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biomisc_R: a repository of command line bioinformatic scripts written in R
while R is a very beginner friendly and popular programming language in bioinformatic circles, there are not many repositories that contain command line scripts that can be easily used. Thats why I created biomisc_R a repository that contains scripts involved in single/multi-fasta/pdb file manipulations, sequence statistics and differential expression analysis. The scripts have been tested on windows 10 build 19041.985 and ubuntu 18.04 with R 3.6.3. if you have any questions and suggestions please let me know!
What are some alternatives?
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
hermiter - Efficient Sequential and Batch Estimation of Univariate and Bivariate Probability Density Functions and Cumulative Distribution Functions along with Quantiles (Univariate) and Nonparametric Correlation (Bivariate)
clustifyr - Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
sjPlot - sjPlot - Data Visualization for Statistics in Social Science
drake - An R-focused pipeline toolkit for reproducibility and high-performance computing
rhmmer - Simple R utilities for working with HMMER
reprex - Render bits of R code for sharing, e.g., on GitHub or StackOverflow.
drugfindR - Repository holding the code for the drugfindR R package
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