isinaltinkaya

the-book-of-secret-knowledge

A collection of inspiring lists, manuals, cheatsheets, blogs, hacks, one-liners, cli/web tools and more.

wttr.in

:partly_sunny: The right way to check the weather

pyprobml

Python code for "Probabilistic Machine learning" book by Kevin Murphy

github-issue-templates

🔣 A collection of GitHub issue, pull request and security templates

vim-markdown

Markdown for Vim: a complete environment to create Markdown files with a syntax highlight that doesn't suck!

Markdown-Tutorial

A comprehensive guide to Markdown / Introduction to Markdown

hap.py

Haplotype VCF comparison tools

templates

Document templates for open-source projects (README, CONTRIBUTING, GitHub templates)

cols4all

Colors for all (R package)

karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

cpp-text-table

C++ text table: format text in tabular form

smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config

ohana

mixture classification, constraint optimization, outlier detection, population structure, admixture history, and selection detection.

VCF2Dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

my-book-library

my books organized by topics

manjaro-i3wm

Personalized Manjaro i3wm configuration

msbwt

A python toolkit for building and querying multi-string BWTs

vcf2sfs

R functions for generating site frequency spectra (SFS) from a VCF file.

analysis

Analysis of inference methods on standard population models

VCF2Dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

Guide-to-manipulating-PLINK-EIG-and-VCF-files

A guide to manipulating genotypic data across the common formats: VCF, EIGENSTRAT and PLINK (PACKEDPED) files. Includes how to convert between formats, merge datasets or subset by individuals in each of the formats.

farm-notes

notes on the farm cluster

CBioInfCpp-0-

The lib CBioInfCpp.h contains 3 groups of functions for C++: "Input-Output", "Working with strings", "Working with graphs". Data structures "Adjacency vector" and "Adjacency map" are implemented in the last one (i.e. in "Working with graphs"). See About_CBioInfCpp for details.

typeloader

CopenhagenTutorial

Tutorial of population genetics for Copenhagen 2021 course students

docwiki

Wiki page for some documentation of tools, including those developed by others

PG_2018

GQuery

GQuery is a software tool for rapidly querying large numbers of bgzip compressed, tabix indexed genomic data files e.g. vcf, maf, bed, bedGraph, etc. from multiple species with different genome builds without the need to develop, debug, and maintain custom file parsers. Search for particular germline or somatic mutations, copy number changes, differentially expressed genes, epigenetic marks, anything that can be associated with genomic coordinates. Just point the GQuery indexer at a collection of tabix indexed files and then run either the GQuery command line app or the web API to search them. GQuery is built using a fast, multi-threaded, genomic range search engine with extensive junit testing.

Tjarno

Demographic inferences from NGS data

bcftools-hacks