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2020-mrna_seq_workshop

Focused multi-day workshop covering the material needed for a successful RNA-Seq experiment.

atlas

ATLAS - Three commands to start analysing your metagenome data

bacterial-carbon-flux-qsip

basalt

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bioinformatics-workshop

RNA-seq Tutorial

boxplotr.shiny

shiny application to generate box plots with R

buckley_lab_sip_project_protocols

Buckley Lab Protocols

combat-seq

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

genomeanalysisr

This is a repo for Human Genome Analysis in R

global-bacterial-diversity-in-wwtps

htssip

An R package for analyzing high throughput sequence stable isotope probing data

icamp1

Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis (Version 1)

map-and-microbial-growth

matafiler

Metagenomic assembly, genome reconstruction and functional as well as taxonomic profiling

picrust2

Code, unit tests, and tutorials for running PICRUSt2

qsip-bram

R package to perform calculations on data produced from quantitative stable isotope probing (qSIP) experiments

rarefaction

Rarefaction scripts

rna-seq-analysis

RNAseq analysis notes from Ming Tang

rnavis

Shiny application to Visualize RNAseq data

sam2counts

Count number of mapped reads per reference in SAM files (often for RNA-Seq experiments)

scrna_shiny

scRNA-seq Shiny App

sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

stamp

Statistical Analysis of Metagenomic Profiles

warming_ak

pipeline for RNA-seq of soil

warming_soil_biodiversity