Vileu

Vileu's Stars

• rstudio/cheatsheets

  Posit Cheat Sheets - Can also be found at https://posit.co/resources/cheatsheets/.

  Language:TeX5.8k23301.8k

• OpenGene/fastp

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  Language:C++1.9k49512332

• samtools/samtools

  Tools (written in C using htslib) for manipulating next-generation sequencing data

  Language:C1.6k1021.3k576

• ncbi/sra-tools

  SRA Tools

  Language:C1.1k56844243

• COMBINE-lab/salmon

  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

  Language:C++76239821160

• DerrickWood/kraken2

  The second version of the Kraken taxonomic sequence classification system

  Language:C++70129821269

• weizhongli/cdhit

  Automatically exported from code.google.com/p/cdhit

  Language:Perl63128133127

• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  Language:Python55618498106

• marbl/Krona

  Interactively explore metagenomes and more from a web browser.

  Language:JavaScript46239177102

• hyattpd/Prodigal

  Prodigal Gene Prediction Software

  Language:C430269785

• bxlab/metaWRAP

  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

  Language:Shell38717539189

• Ecogenomics/CheckM

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

  Language:Python3321437773

• jenniferlu717/Bracken

  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

  Language:C++2791424950

• kevinsblake/NatParksPalettes

  Color palette package inspired by National Parks

  Language:R227244

• conda-incubator/conda-tree

  conda dependency tree helper

  Language:Python15951712

• BinPro/CONCOCT

  Clustering cONtigs with COverage and ComposiTion

  Language:Python122822549

• YongxinLiu/EasyMicrobiome

  Language:C804332

• HadrienG/tutorials

  :books: Various bioinformatics tutorials

  566838

• castelao/seabird

  Python parser for Sea-Bird CTD outputs, usually .cnv files.

  Language:Python4776229

• Linwei-Wu/warming_soil_biodiversity

  Language:R192011

• mgtools/MinPath

  MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset.

  Language:C18289

• EMSL-Computing/CoreMS-Portal

  Language:JavaScript70

• EMSL-Computing/Day3-EMSL-SummerSchool-2022

  Language:Jupyter Notebook41

• microbiomedata/enviroMS

  Language:Python4880

• ramalok/mitags_extraction_protocol

  mitags extraction protocol

  41

• clagovaldivia/genome-project

  Language:HTML3

• danczakre/EMSL2022_Visualization

  Contains all of the files and scripts necessary to participate in the EMSL Summer School 2022 Visualization walkthrough

  Language:R30

• andreamentges/functional-diversity-index

  Calculating functional molecular diversity of marine dissolved organic matter in MATLAB

  Language:MATLAB2100

• nikhilg123/Module_5_metagenome_assembly-MAGs

  2

• EricRaes/Time-series-Analyses

  Code for plotting the figures in the marine time-series manuscript

  Language:R11