TheOafidian

TheOafidian's Stars

• rsnapshot/rsnapshot

  a tool for backing up your data using rsync (if you want to get help, use https://lists.sourceforge.net/lists/listinfo/rsnapshot-discuss)

  Language:Perl3.3k87215263

• Ecogenomics/CheckM

  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

  Language:Python3531438073

• arpcard/rgi

  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

  Language:Python3412024878

• lh3/miniprot

  Align proteins to genomes with splicing and frameshift

  Language:C34086218

• wwood/CoverM

  Read coverage calculator for metagenomics

  Language:Rust3131116731

• ncbi/amr

  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

  Language:C++2812912441

• marbl/Winnowmap

  Long read / genome alignment software

  Language:C266154723

• mhammell-laboratory/TEtranscripts

  A package for including transposable elements in differential enrichment analysis of sequencing datasets.

  Language:Python2371921031

• veg/hyphy

  HyPhy: Hypothesis testing using Phylogenies

  Language:HyPhy225221.4k69

• nf-core/mag

  Assembly and binning of metagenomes

  Language:Nextflow223161306113

• AnantharamanLab/VIBRANT

  Virus Identification By iteRative ANnoTation

  Language:Python154510038

• qiyunlab/HGTector

  HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.

  Language:Python131109535

• EBI-Metagenomics/emg-viral-pipeline

  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

  Language:Python12877216

• lh3/ropebwt3

  BWT construction and search

  Language:C106643

• hoelzer-lab/rnaflow

  A simple RNA-Seq differential gene expression pipeline using Nextflow

  Language:HTML96414820

• jolespin/veba

  A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

  Language:Python814469

• nf-core/differentialabundance

  Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq

  Language:Nextflow6715018341

• EBI-Metagenomics/mettannotator

  Language:Python57555

• rvicedomini/strainberry

  Automated strain separation of low-complexity metagenomes

  Language:Python512115

• YuLab-SMU/MicrobiomeProfiler

  :microbe: A shiny package for microbiome functional enrichment analysis

  Language:R37437

• bagrow/network-portrait-divergence

  An information-theoretic, all-scales approach to comparing networks

  Language:Python302315

• CAMI-challenge/AMBER

  AMBER: Assessment of Metagenome BinnERs

  Language:Python288337

• Russel88/MAGinator

  MAGinator - Accurate SNV calling and profiling of MAGs

  Language:Python192121

• Boehringer-Ingelheim/dso

  Data Science Operations (dso) command line tool

  Language:Python137300

• biobakery/MMUPHin

  MMUPHin: Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

  Language:R8504

• PASTA-ELN/pasta-eln

  PASTA-ELN with new frontend

  Language:Python801652

• ramellose/anuran

  Toolbox for identification of non-random associations

  Language:Python6121

• thomazbastiaanssen/Volatility

  Language:R6200

• ClarkLaboratory/IsoLamp

  Isoform discovery from long-read amplicon sequencing data

  Language:Shell31

• HaploKit/StrainXpress

  StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high complexity metagenome sequencing data at strain resolution.

  Language:C++1000