A list of alternative splicing analysis resources

A fast, alignment-free method for estimating sequence conservation using protein sequence embedding

Software tool for the flexible design of pegRNAs and ngRNAs for prime editing!

Automatically identify non-interfering nucleotide linkers between a pegRNA and 3' motif

Some Rosetta Scripts that allow for various simple tasks

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

ggpie - A ggplot2 extension to create pie, donut and rose pie plot

Another Gtf/Gff Analysis Toolkit

Build and run containers leveraging NVIDIA GPUs

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

annotate a VCF with other VCFs/BEDs/tabixed files

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

A computational workflow for exitron splicing identification

Prediction of Binding Residues in Disordered Regions Based on Protein Embeddings; TUM Master Praktikum Bioinformatics 2022 (Project #3) and Master's Thesis

ClinVar Mapping and Annotation Toolkit

A machine learning based protein disorder predictor.

Open source code for AlphaFold.

Jupyter Notebook Conversion

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.

A collection of scripts and notes related to genomics and bioinformatics

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…