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mvp

A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study

ngs

Scripts for next generation sequencing

ngs-1

Next Generation Shell (NGS)

note

oc-gen-x

OpenCore Config Generator

pairwisecomparisons

Pairwise comparison tests for one-way designs 🔬📝

parameters

:bar_chart: Computation and processing of models' parameters

performance

:muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)

pheatmap

Pretty heatmaps

phylo_wrapper_scripts

Scripts to help automate various phylogenetic or phylogeography programs (Admixture, RAxML, CLUMPP + DISTRUCT). Also includes a script for replacing sample or taxon names in input files.

phyloseq_translate

phyloseq R

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

plotting-tree-with-data-using-ggtreeextra

pophelper

An R package to analyse and visualise admixture proportions from STRUCTURE, fastSTRUCTURE, TESS, ADMIXTURE etc.

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

practical-applications-in-r-for-psychologists

Lesson files for Practical Applications in R for Psychologists.

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

qiime16stutorial

A tutorial on methods of 16S analysis with QIIME 1

qiime2

Official repository for the QIIME 2 framework.

qiime2chinesemanual

QIIME 2中文文档(QIIME 2 Chinese Manual)

qiime2r

Import qiime2 artifacts to R

rdptools

Collection of commonly used RDP Tools for easy building

reactomepa

Reactome Pathway Analysis

report

:scroll: :tada: Automated reporting of objects in R

reseqtools

A Toolkit for analyzing next-generation DNA Re-Sequencing data

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

rush

A cross-platform command-line tool for executing jobs in parallel

samtools

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

sequencing-analysis-with-dada2

16s rRNA data sequencing analysis using DADA2 in QIIME2 and Mothur