KatjaKo

KatjaKo's Stars

• NBISweden/workshop-reproducible-research

  NBIS/ELIXIR course: Tools for Reproducible Research

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• eggnogdb/emapper-benchmark

  Raw data and scripts used to benchmark eggnog-mapper. Analysis and additional tests cases are provided as a python notebook.

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• mikemc/speedyseq

  Speedy versions of phyloseq functions

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• benjjneb/dada2

  Accurate sample inference from amplicon data with single nucleotide resolution

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• transcript/samsa2

  SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.

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• NBISweden/contigtax

  Taxonomic classification of metagenomic contigs

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• paul-buerkner/brms

  brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan

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• tidyverse/ggplot2

  An implementation of the Grammar of Graphics in R

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• MG-RAST/pipeline

  The MG-RAST pipeline

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• cran/taxonomizr

  :exclamation: This is a read-only mirror of the CRAN R package repository. taxonomizr — Functions to Work with NCBI Accessions and Taxonomy Report bugs for this package: https://github.com/sherrillmix/taxonomizr/issues

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• thelovelab/DESeq2

  Differential expression of RNA-seq data using the Negative Binomial

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• KlausVigo/phangorn

  Phylogenetic analysis in R

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• shandley/Microbiome-Analysis-Using-R

  Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.

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• benjjneb/ITS-Workflow

  A descriptory pipeline for processing ITS Samples using DADA2

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• benjjneb/LRASManuscript

  Reproducible Analyses accompanying DADA2 + PacBio Manuscript

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• karthik/wesanderson

  A Wes Anderson color palette for R

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• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

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• tseemann/PEAR

  Pair-End AssembeR

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• bbuchfink/diamond

  Accelerated BLAST compatible local sequence aligner.

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• grunwaldlab/metacoder

  Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

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• donovan-h-parks/STAMP

  Statistical Analysis of Metagenomic Profiles

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• MG-RAST/MG-RAST-Tools

  Repository of script tools, examples, and contributed code for using the MG-RAST API

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• MG-RAST/matR

  Metagenomics Analysis Tools

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• 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:

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• MG-RAST/MG-RAST

  The MG-RAST Backend -- the API server

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