TCGAbiolinks
dada2
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| TCGAbiolinks | dada2 | |
|---|---|---|
| 2 | 1 | |
| 276 | 449 | |
| 2.9% | - | |
| 4.6 | 4.3 | |
| 19 days ago | 3 months ago | |
| R | R | |
| - | GNU Lesser General Public License v3.0 only |
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.
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
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.
What are some alternatives?
bambu - Reference-guided transcript discovery and quantification for long read RNA-Seq data
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
maftools - Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
awesome-R - A curated list of awesome R packages, frameworks and software.
MicrobiomeStat - Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
ggplot2 - An implementation of the Grammar of Graphics in R
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite