SIJAE-WOO

TRACKPOSON

Pipeline to detect transposable elements (TEs) insertions polymorphism

TransposonUltimate

TransposonUltimate - a holistic set of tools for transposon identification

arriba

Fast and accurate gene fusion detection from RNA-Seq data

FriendsDontLetFriends

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

pylustrator

Visualisations of data are at the core of every publication of scientific research results. They have to be as clear as possible to facilitate the communication of research. As data can have different formats and shapes, the visualisations often have to be adapted to reflect the data as well as possible. We developed Pylustrator, an interface to directly edit python generated matplotlib graphs to finalize them for publication. Therefore, subplots can be resized and dragged around by the mouse, text and annotations can be added. The changes can be saved to the initial plot file as python code.

stable-diffusion

cloneMap

An R package to plot maps of clone distributions in somatic evolution

vastdb_framework_code_example

Markdown document for the case example on the use of the VastDB framework in Methods in Molecular Biology.

hts-specs

Specifications of SAM/BAM and related high-throughput sequencing file formats

SVRare-GEL

To discover rare structural variants from whole genome sequencing data

2021Z-DataVisualizationTechniques

📊 Data Visualization Techniques course for DS studies in Winter 2020/21

DGE_workshop

hail

Cloud-native genomic dataframes and batch computing

Mathematics-for-ML

🧮 A collection of resources to learn mathematics for machine learning

flopp

flopp is a software package for single individual haplotype phasing of polyploid organisms from long read sequencing.

lab_automation_tools

Collection of lab automation scripts, tools, and other resources for liquid handling systems, etc.

scanpy

Single-cell analysis in Python. Scales to >1M cells.

STREAMLINE

Simple Transparent End-To-End Automated Machine Learning Pipeline for Supervised Learning in Tabular Binary Classification Data

Pangolin

Pangolin is a deep-learning method for predicting splice site strengths.

REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats

vg

tools for working with genome variation graphs

learning_vcf_file

Learning the Variant Call Format

scxa-workflows

Higher level repo for aggregating all of Atlas workflow logic for Single Cell

branchpointer

MaxEntScan

suport to maxentscan program on python script

ExpansionHunter

A tool for estimating repeat sizes

LaBranchoR

Reproduce the LaBranchoR

CalliNGS-NF

GATK RNA-Seq Variant Calling in Nextflow

GenePy-1.4

Latest GenePy version using Ensembl VEP annotation, gnomAD random forest flag. Incorporation of tri-allelic variants *in progress*

vcf2prot

Accelerate the generation of personalized proteomes from a Variant calling format (VCF) file and a reference proteome using graphical processing units (GPUs).