mischalundberg Goto Github PK

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

cause

R package for CAUSE

ch-methylation

Portable Calculator for CH methylation (PoCalCH) handles .fasta files. The given sequences are cleaned from not needed line breaks and the CH methylation within the given sequences is calculated. As output PoCalCH delivers a Word file and an Excel sheet. All user interactions happen in an easy to use GUI. Its key strength is its tested reliability, portability and time saving during analysis.

chmethylation

Portable Calculator for CH methylation (PoCalCH)

cpg_methylation_pipeline

custom_gwas

Python Code using CyVCF2 to run custom GWAS models on imputed VCF files

dna_reverse_complement

Portable Reverse Complementing (PoRC) tool is an easy to use tool for combining and autonomously reverse-complementing sequences. It guarantees a consistency throughout each evaluation due to a test driven development approach. The ability to run tasks like combining several sequences, cutting the not needed line breaks and reverse complementing the sequences in just one step with the Output saved into several formats, saves researchers valuable time while evaluating data and is the key strength of PoRC. PoRC handles ambiguous and unambiguous DNA sequences with the IUPAC ambiguity code in .fasta or .seq format.

extract_sequences

Python code to extract sequences from sequencing (e.g. fasta/bisulfite) files.

friendsdontletfriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

git-101

Introduction to Version Control with Git

gripper

Find non-reference processed pseudogene insertions from discordant read pair mappings

gt-dimred

Genotype dimension reduction research. Code for manuscript "UMAP reveals cryptic population structure and phenotype heterogeneity in large genomic cohorts"

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

imapsync

Imapsync is an IMAP transfers tool. The purpose of imapsync is to migrate IMAP accounts or to backup IMAP accounts. IMAP is one of the three current standard protocols to access mailboxes, the two others are POP3 and HTTP with webmails, webmails are often tied to an IMAP server. Upstream website is

itis

tool to Identify TE Insertion Sites in genome

jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.

ldsc

LD Score Regression (LDSC)

locuszoom-standalone

Create regional association plots from GWAS or meta-analysis

m1_scripts_of_gwas_and_downstream_analayses

Scripts used for analysis previous to my M1

mrinstruments

Data objects for various sets of instruments

nanopolish

Signal-level algorithms for MinION data

nshg-pm2023_johnshorter

Resources for the PGS PRS workshop

nshg2023_mrworkshop_gumeo

perf

PERF is an Exhaustive Repeat Finder

phesant

PHESANT - PHEnome Scan ANalysis Tool (pheWAS, Mendelian randomisation (MR)-pheWAS etc.) in UK Biobank

pydio-core

Pydio 8 official repository

pyicecat

rdpwrap

RDP Wrapper Library

rdpwrap-1

RDP Wrapper Library

rye

:herb: :bread: Large scale ancestry inference from PCA data