TillBirkner / metadeconfoundR
☆18Updated 2 months ago
Alternatives and similar repositories for metadeconfoundR:
Users that are interested in metadeconfoundR are comparing it to the libraries listed below
- ☆50Updated last year
- Metagenomics-related extended functionalities to samtools☆21Updated last year
- Pipeline for metagenome and metatranscriptome joint assembly☆21Updated 2 years ago
- MaAsLin3: Microbiome Multivariate Association with Linear Models☆33Updated last month
- CroCoDeEL is a tool that detects cross-sample contamination in shotgun metagenomic data☆24Updated 3 weeks ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆45Updated last year
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆45Updated 5 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆57Updated last week
- scripts for estimating bacteria replication rates based on population genome copy number variation☆72Updated 5 years ago
- A toolkit for prokaryotic comparative genomics☆47Updated 3 months ago
- ☆52Updated last year
- Growth Rate Index (GRiD) measures bacterial growth rate from reference genomes (including draft quality genomes) and metagenomic bins at …☆32Updated 4 years ago
- AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resis…☆35Updated last month
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.☆25Updated 6 months ago
- MuDoGeR makes the recovery of genomes from prokaryotes, viruses, and eukaryotes from metagenomes easy.☆88Updated 8 months ago
- Batch effects removal for microbiome data via conditional quantile regression☆27Updated 2 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆46Updated 3 years ago
- IS mapping software☆53Updated 3 years ago
- Analysing Metagenomic Species (MGS)☆41Updated 4 years ago
- Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis☆14Updated 3 weeks ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆29Updated last year
- Downstream processing of VAMB binning for Viral Elucidation☆49Updated 9 months ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated 2 years ago
- MetaCompare☆17Updated last year
- Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data☆14Updated last month
- ☆69Updated last month
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆59Updated last week
- BEAV: Bacterial Element Annotation reVamped☆64Updated 5 months ago
- A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets☆26Updated 3 months ago