isinaltinkaya

awesome-pipeline

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

ThinkBayes2

Text and code for the forthcoming second edition of Think Bayes, by Allen Downey.

esquisse

RStudio add-in to make plots interactively with ggplot2

getting-started-with-genomics-tools-and-resources

Unix, R and python tools for genomics and data science

learning-bioinformatics-at-home

resources for learning bioinformatics

XiaoMiToolV2

XiaomiTool V2 - Modding tool for xiaomi devices

TaskerSettings

Helper app for Tasker

ForceDoze

Enable Doze mode immediately after screen off and turn off motion sensing to get best battery life

eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

genmap

GenMap - Fast and Exact Computation of Genome Mappability

TheHumanPangenome

A Strategy for Building and Using a Human Reference Pangenome

BAMscale

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

hpgp-data

Data from the Human PanGenomics Project

bio_tools

Useful bioinformatic scripts

HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies

vcf2fasta

Converts a VCF file to a FASTA alignment provided a reference genome and a GFF file

sequenceTools

PCAone

Fast Principal Component Analysis All in One

treeseq-inference

Work for the tree sequence inference paper.

rd-imputation-accuracy

Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.4, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correlation), Concordance.

bai-indexer

Build an index for your BAM Index (BAI)

snakemake-parallel-bwa

A Snakefile to parallelize bwa.

biol610

intro to programming for IE2 evolution students

imputation-pipeline

htslib-plugins

Plugins for use with HTSlib

www.htslib.org

The http://www.htslib.org/ web site

it-docs

Docs for RacimoLab IT resources

ngsClean-1

Pipeline for NGS read (filtering, trimming, merging) and SNP (quality, depth, biases, ...) quality control

ANGSD-asso-scripts

ANGSD_scripts

Scripts for help running ANGSD and post-ANGSD analyses