drugfindR
biomisc_R
| drugfindR | biomisc_R | |
|---|---|---|
| 1 | 3 | |
| 7 | 23 | |
| - | - | |
| 9.4 | 0.0 | |
| 5 days ago | almost 2 years ago | |
| R | R | |
| GNU General Public License v3.0 only | MIT License |
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drugfindR
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Favorite R fun fact
I named drugfindR for precisely the same reason. :D
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)
Baltica - Baltica: integrated differential junction usage
sjPlot - sjPlot - Data Visualization for Statistics in Social Science
cosmosR - COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
rhmmer - Simple R utilities for working with HMMER
maftools - Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
rna-seq-kallisto-sleuth - A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.