CHoeltermann

nextflow

A DSL for data-driven computational pipelines

Intro_to_GWAS

An introductory workshop to GWAS analysis using PLINK and R

ADMIXTURE-smartPCA-PLINK-and-EIGENSOFT

Scripts and notes on how to analyse ancient DNA genotype data to understand population structure

rnavar

gatk4 RNA variant calling pipeline

plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

plink

(Genomics) Dockerfile for running plink v1 - http://pngu.mgh.harvard.edu/~purcell/plink/

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

variant-calling-pipeline-gatk4

Variant Calling Pipeline Using GATK4 and Nextflow

SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data

gatk4-jupyter-notebook-tutorials

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

biobakery

bioBakery tools for meta'omic profiling

Patchwork

Alignment-based retrieval and concatenation of phylogenetic markers from whole genome sequence (WGS) data

ggcoverage

Visualize and annotate genomic coverage with ggplot2

EDTA

Extensive de-novo TE Annotator

Parsing-RepeatMasker-Outputs

Few scripts facilitating the extraction of info from Repeat Masker .out files

fgsea

Fast Gene Set Enrichment Analysis

TransposonUltimate

TransposonUltimate - a holistic set of tools for transposon identification

VariabilityInTEs

TEtranscripts

A package for including transposable elements in differential enrichment analysis of sequencing datasets.

rm2gff3

Convert RepeatMasker ".out" file into a gff3 with colors!!!

repeatcraftp

meta-pipeline for repetitive element de-fragmentation and annotation

Mosaic-cis-regulatory-evolution-drives-transcriptional-partitioning-of-HERVH-endogenous-retrovirus..

Relevant files, scripts, detailed methods for work done by Thomas A. Carter

biomaRt

R package providing query functionality to BioMart instances like Ensembl

rnaseq

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

nb_conda_kernels

Package for managing conda environment-based kernels inside of Jupyter

ipykernel

IPython Kernel for Jupyter