scwatts / fastspar
Rapid and scalable correlation estimation for compositional data
☆87Updated 11 months ago
Alternatives and similar repositories for fastspar:
Users that are interested in fastspar are comparing it to the libraries listed below
- Statistical analysis for sparse high-throughput sequencing☆69Updated 4 months ago
- This is the source code for multisamples ARGs profiling using SARG2.0 database☆46Updated 4 years ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆30Updated 2 years ago
- Metatranscriptomics Tutorial☆62Updated last year
- All of my various bioinformatic scripts fit for public consumption (loosely defining "fit")☆73Updated 2 years ago
- Scripts and tutorials on how to assemble individual microbial genomes from metagenomes☆80Updated 8 years ago
- Course material for the metagenomics course☆44Updated 3 years ago
- From genomes to phenotypes: Traitar, the microbial trait analyzer☆59Updated 5 years ago
- Generating iToL annotations from Spreadsheet or CSV files☆100Updated 4 years ago
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆57Updated last year
- Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing☆115Updated 11 months ago
- Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data☆155Updated 2 years ago
- Nextflow pipeline to analyze PacBio HiFi full-length 16S data☆75Updated 2 months ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆54Updated 3 years ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆59Updated 4 years ago
- ☆48Updated 4 years ago
- ☆82Updated last year
- Statistical Analysis of Metagenomic Profiles☆93Updated 5 years ago
- ☆74Updated last year
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆46Updated 3 years ago
- Reproducible Analyses accompanying DADA2 + PacBio Manuscript☆33Updated 4 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- r package for post-clustering curation of amplicon next generation sequencing data (metabarcoding)☆65Updated last year
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- R implementation of the LEfSe method☆58Updated last week
- Snakemake workflow for metagenomic classification with Kraken2☆65Updated last year
- Horizontal gene transfer (HGT) identification pipeline☆57Updated last year
- Amplicon sequencing pipelines suitable for SSU (16S, 18S), LSU (23S, 28S) and ITS.☆53Updated 3 months ago
- GET_HOMOLOGUES: a versatile software package for pan-genome analysis☆114Updated 2 months ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆85Updated last year