gopuraja

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

atacseq

ATAC-seq peak-calling and QC analysis pipeline

koeken

A Linear Discriminant Analysis Effect Size (LEfSe) wrapper.

MicrobiotaProcess

:microbe: A comprehensive R package for deep mining microbiome

dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

LightGBM

A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.

DAT8

General Assembly's 2015 Data Science course in Washington, DC

awesome-rshiny

An awesome R-shiny list!

yart

RMarkdown Template for writing PDF reports

reactable

Interactive data tables for R

biocode

Bioinformatics code libraries and scripts

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

yingtools2

Ying's tools for analysis, with particular focus on microbiome data

MicrobiomeAnalystR

A companion R package for the MicrobiomeAnalyst web server

metamicrobiomeR

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models

MetaboDiff

metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds

epiviz

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

shopping-list-vanillajs-pouchdb

Shopping List is an Offline First demo Progressive Web App built using Vanilla JS and PouchDB.

fastbook

The fastai book, published as Jupyter Notebooks

OrchestratingSingleCellAnalysis-release

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

humann

HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

pcc_2e

Online resources for Python Crash Course (Second Edition), from No Starch Press

omicsplayground

Visual self-service analytics platform for big omics data.

nextflow-demos

Example Nextflow pipelines and programming techniques

tmux

tmux source code

bpnet

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data