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**Metaxa2**: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data
https://microbiology.se/software/metaxa2/
[doi:10.1111/1755-0998.12399](https:…
vmikk updated
3 months ago
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Hi, I would like to use DeepMicro for disease prediction.
But i can't figure out how to generate the 'correct' input data for DeepMicro. I saw that the UserDataExample.csv has a lot of digits, wher…
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when i do mpse3
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Very exciting work!
I want to give it a go with my own marker genes database.
The publication states 'SameStr can be easily adapted for use with [...] alternative, user-provided, marker sequences.'
…
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mpse1 %>%
mp_cal_abundance(.abundance=Abundance, force=TRUE, relative=FALSE) %>%
mp_diff_analysis(.abundance=Abundance, force=TRUE, relative=FALSE, .group=group, filter.p="pvalue",p.adjust = "…
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The MetaPhlAn series of taxonomic classifiers are very popular in metagenomics, and have very low overhead. It also allows exporting of physical alignments to the gene databases that theoretically (bu…
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Dear developer(s),
I am new to the biobakery VM images and currently I am going through the biobakery_workflows tutorials following:
https://github.com/biobakery/biobakery/wiki/biobakery_workflo…
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- BBDUK
- HOSTREMOVAL
- MALT/KRAKEN
- MALTEXTRACT
- KRAKENPARSE
## New
- Option: mapped OR unmapped reads to metagenomic screeming
- KRAKENUNIQ
- METAPHLAN3
- PRINSEQ (alternative comple…
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Dear MPSE developer,
Recently I try to use MicrobiotaProcess to do microbiome data analysis. This is a very nice R package as far as I know.
So, I installed it and learn it based on the [documen…
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The metaphlan pipeline is providing only the relative abundance assay, and not counts. This is sometimes inconvenient for various standard metagenomic analysis methods and workflows that expect counts…