dada2
MicrobiomeStat
dada2 | MicrobiomeStat | |
---|---|---|
1 | 1 | |
484 | 36 | |
1.0% | - | |
6.7 | 9.3 | |
30 days ago | 22 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.
MicrobiomeStat
What are some alternatives?
GTDBTk - GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
sjPlot - sjPlot - Data Visualization for Statistics in Social Science
kraken-biom - Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
tableone - R package to create "Table 1", description of baseline characteristics with or without propensity score weighting
TCGAbiolinks - TCGAbiolinks
lmtp - :package: Non-parametric Causal Effects Based on Modified Treatment Policies :crystal_ball:
rBLAST - Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
easystats - :milky_way: The R easystats-project
MMseqs2 - MMseqs2: ultra fast and sensitive search and clustering suite
renjin - JVM-based interpreter for the R language for the statistical analysis.
seqinr - Biological sequences retrieval and analysis
empress - A fast and scalable phylogenetic tree viewer for microbiome data analysis