rajaldebnath
Microbial ecology | Microbiology | Bioinformatics https://scholar.google.com/citations?user=hiB40poAAAAJ&hl=en
Central Silk BoardIndia
rajaldebnath's Stars
chubin/wttr.in
:partly_sunny: The right way to check the weather
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
crazyhottommy/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
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:
malonge/RagTag
Tools for fast and flexible genome assembly scaffolding and improvement
bxlab/metaWRAP
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
fbreitwieser/pavian
🌈 Interactive analysis of metagenomics data
jtamames/SqueezeMeta
A complete pipeline for metagenomic analysis
ncbi/pgap
NCBI Prokaryotic Genome Annotation Pipeline
wwood/CoverM
Read coverage calculator for metagenomics
dzerbino/velvet
Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
DaehwanKimLab/centrifuge
Classifier for metagenomic sequences
fbreitwieser/krakenuniq
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
ropensci/biomartr
Genomic Data Retrieval with R
ropensci/rentrez
talk with NCBI entrez using R
egeulgen/pathfindR
pathfindR: Enrichment Analysis Utilizing Active Subnetworks
PacificBiosciences/pb-metagenomics-tools
Tools and pipelines tailored to using PacBio HiFi Reads for metagenomics
sunbeam-labs/sunbeam
A robust, extensible metagenomics pipeline
adw96/DivNet
diversity estimation under ecological networks
Bioconductor/BiocWorkshops
:warning: 2018 :warning: Bioconductor Workshops
FrederickHuangLin/ANCOM-Code-Archive
Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.
jessesadler/intro-to-r
Scripts and data to go along with introductions to R
iquasere/KEGGCharter
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
filipematias23/cleanRfield
cleanRfield: This package is a compilation of functions to clean and filter observations from yield monitors or other agricultural spatial point data. Yield monitors are prone to error, and filtering the observations or removing observations from near field boundaries can improve estimates of whole-field yield, combine speed, grain moisture, or other parameters. In this package, users can easily select filters thresholding for one or more traits and prepare a smaller dataset to make decisions.
mahendra-mariadassou/phyloseq-extended
Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul
leffj/mctoolsr
Microbial community analysis tools in R
DenefLab/MicrobeMiseq
Set of useful functions and scripts for analyzing amplicon Miseq data.
tanaes/snakemake_anvio
snakemake rules for running anvio
rajaldebnath/co-occurrence
R scripts for performing co-occurrence analyses
rajaldebnath/RNASeq_Trinity_Tuxedo_Workshop
materials for the RNA-Seq workshop on Trinity and Tuxedo, covering de novo and genome-guided transcript assembly and downstream analysis.