Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological samples | ||
| Stool samples from ME/CFS patients and healthy donors | This study | N/A |
| Plasma samples from ME/CFS patients and healthy donors | This study | N/A |
| Critical commercial assays | ||
| QIAamp 96 DNA QIAcube HT Kit | QIAGEN | #51331 |
| BioCollector fecal collection kit | The BioCollective, Denver, CO | https://www.thebiocollective.com/products-services |
| OMNIgene•GUT tube | DNA Genotek | OMR-200 |
| Deposited data | ||
| Metagenomics sequencing raw data | This study | NCBI-SRA: Bioproject PRJNA878603 |
| Software and algorithms | ||
| R version (v4.0.4) | ||
| Python (v3.10.4) | ||
| scythe (v0.994) | Buffalo, 2014 | https://github.com/vsbuffalo/scythe |
| sickle (v1.33) | Joshi and Fass, 2011 | https://github.com/najoshi/sickle |
| MetaPhlAn3 | Beghini et al., 2021 | https://huttenhower.sph.harvard.edu/metaphlan/ |
| Bowtie2 (v2.3.1) | Langmead and Salzberg, 2012 | https://github.com/BenLangmead/bowtie2 |
| GRiD (v1.3) | Emiola et al., 2018 | https://github.com/ohlab/GRiD |
| USEARCH (v8.0.1517) | Edgar, 2010 | https://www.drive5.com/usearch/ |
| dplyr_1.0.5 | R package | https://dplyr.tidyverse.org/index.html |
| microbiome_1.12.0 | R package | https://microbiome.github.io/tutorials/ |
| phyloseq_1.34.0 | R package | https://joey711.github.io/phyloseq/ |
| maaslin2_1.8.0 | R package | https://huttenhower.sph.harvard.edu/maaslin/ |
| globaltest_5.44.0 | R package | https://www.bioconductor.org/packages/release/bioc/html/globaltest.html |
| bcdstats_0.0.0.9005 | R package | https://github.com/bcdudek/bcdstats/ |
| lme4_1.1–29 | R package | https://cran.rproject.org/web/packages/lme4/index.html |
| vegan_2.6–2 | R package | https://cran.r-project.org/web/packages/vegan/index.html |
| deseq2_v1.18.1 | R package | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| scipy_1.8.0 | python package | https://scipy.org/ |
| jupyter_4.9.2 | python package | https://jupyter.org/ |
| numpy_1.22.3 | python package | https://numpy.org/ |
| pandas_1.4.2 | python package | https://pandas.pydata.org/ |
| scikit-learn_1.0.2 | python package | https://scikit-learn.org/stable/index.html |