dada2
TCGAbiolinks


dada2 | TCGAbiolinks | |
---|---|---|
1 | 2 | |
485 | 305 | |
1.0% | 1.6% | |
6.7 | 5.1 | |
12 days ago | 14 days ago | |
R | R | |
GNU Lesser General Public License v3.0 only | - |
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dada2
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Error model generation and subsequent steps in DADA2 pipeline for multiple sequencing runs
It is recommended to process each run separately (https://github.com/benjjneb/dada2/issues/1177). Each flow cell behaves differently, so the error model for one might not work well for another run. You can merge them together once you have your sequence table.
TCGAbiolinks
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TCGAbiolinks package in R
Perhaps you have a similar issue to this post: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/354. They resolved it by converting their Ensemble IDs to Symbol IDs instead for the plot to work
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Desparate help post regarding the Bioconductor package TCGAbiolinksGUI
Looking at the github page https://github.com/BioinformaticsFMRP/TCGAbiolinks
What are some alternatives?
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
maftools - Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
awesome-R - A curated list of awesome R packages, frameworks and software.
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
ggplot2 - An implementation of the Grammar of Graphics in R
seqinr - Biological sequences retrieval and analysis
r4ds - R for data science: a book

