MaSchCodes

MaSchCodes's Stars

• bioinformatics-centre/kaiju

  Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

  Language:C27467

• AU-ENVS-Bioinformatics/TotalRNA-Snakemake

  A pipeline for TotalRNA analysis

  Language:Jupyter Notebook22

• FrederickHuangLin/ANCOM-BC-Code-Archive

  Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.

  Language:HTML3010

• biozervas/INTERACT_16S_DK_2021

  Additional information in relation to the lab work, sample preparation and sequencing of 16S amplicons of bulk, rhizosphere and rhizoplane soil from 4 wheat cultivars in Denmark.

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• thelovelab/DESeq2

  Differential expression of RNA-seq data using the Negative Binomial

  Language:R36689

• thelovelab/rnaseqGene

  RNA-seq workflow: exploratory analysis and differential expression

  Language:TeX7339

• elfrouin/transcriptM

  Language:Python13

• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  Language:Python579106

• biocore/qurro

  Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

  Language:JavaScript3310

• joey711/phyloseq

  phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

  Language:R591187

• jbisanz/qiime2R

  Import qiime2 artifacts to R

  Language:HTML16052

• biovcnet/biovcnet.github.io

  Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

  Language:HTML5924

• applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics

  Interactive lessons in bioinformatics.

  Language:Python812314

• benjjneb/dada2

  Accurate sample inference from amplicon data with single nucleotide resolution

  Language:R479144

• ShadeLab/NetworkAnalysisWorkflows

  Here is a repo for workflows and notes for Network analyses of microbial data

  Language:R31

• ShadeLab/MetaAnalysis_MicrobesInTime_ISMEJ2013

  R scripts used for calculations in Shade et al. 2013 ISMEJ

  Language:R3

• ShadeLab/ConditionallyRareTaxa

  R scripts and tutorial datasets to detect conditionally rare taxa in time series of microbial communities

  Language:R203

• HRGV/quast

  Genome assembly evaluation tool

  Language:C++1

• HRGV/phyloFlash

  phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

  Language:Perl7926

• zdk123/SpiecEasi

  Sparse InversE Covariance estimation for Ecological Association and Statistical Inference

  Language:R20069

• biovcnet/topic-R

  A repository for the lessons and notebooks used for R tutorials.

  Language:HTML613

• ramellose/mako

  API for setting up a Neo4j database with BIOM files and networks

  Language:Python82

• BlakeRMills/MetBrewer

  Color palette package in R inspired by works at the Metropolitan Museum of Art in New York

  Language:R1.1k82

• geronimp/graftM

  GraftM - Rapid community profiles from metagenomes

  Language:Python4416

• torognes/vsearch

  Versatile open-source tool for microbiome analysis

  Language:C++683124

• anwarMZ/CoMW

  Comparative Metatranscriptomics Workflow

  Language:Python84