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blood_atac

Reanalysis of the ATAC-Seq data from the Corces et al. 2016 paper

coexpression-transeqtl

Analysis source code for co-expression trans-eQTL analysis

coloc

colocwrapper

Helpful functions to streamline colocalisation analysis with coloc

eigenmt

An Efficient Multiple-Testing Adjustment for eQTL Studies that Accounts for Linkage Disequilibrium between Variants

eqtlutils

Collection of reusable R functions for eQTL mapping

flow_cytomtery_genetics

Analysis of macrophage cell surface expression of CD14, CD16 and CD206 proteins using flow cytometry.

hadge

Comprehensive pipeline for donor demultiplexing in single cell

intro-to-rnaseq-hpc-o2

This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster

kauralasoo.github.io

💎 🐳 A super customizable Jekyll theme for personal site, team site, blog, project, documentation, etc.

knitr-example

An example of a genomics analysis using knitr

macrophage-gxe-study

Shared genetic effects on chromatin and gene expression reveal widespread enhancer priming in immune response

macrophage-tuqtls

merge_multistudy_data

This repo is to merge genotype and phenotype daya of multiple datasets having common cell_types

mmseq

Haplotype, isoform and gene level expression analysis using multi-mapping RNA-seq reads

mtat.03.239_bioinformatics

Teaching materials and tutorials for the bioinformatics course thought at the University of Tartu

pivotviewer.py

Tools to create PivotViewer collections in Python.

rasqual

Robust Allele Specific Quantification and quality controL

regenie-nextflow-pipeline

reviseannotations

R package to compare transcript annotations and split them into alternative transcription events.

rmarkdown

Dynamic Documents for R

rnaseq

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

rnaseq_pipeline

Pipeline for downloading and processing published RNA-seq datasets

ryanair-seat-allocation

How random are Ryanair's randomly allocated seats really?

sequtils

Semi-random collection of R functions to work with sequencing data.

txrevise

Construct custom transcript annotations for Salmon

utils

Small scripts and wrapper around tools to deal with genomics data.

wiggleplotr

A small R package to make sequencing read coverage plots in R.

wiggleplotr_old

A tool to create wiggle plots from RNA-Seq in R.

wordocr

Toy example of optical character recognition implemented with OpenCV