whiffen's repositories
alphafold
Open source code for AlphaFold.
arriba
Fast and accurate gene fusion detection from RNA-Seq data
CharGer
Characterization of Germline variants
clusterProfiler
:bar_chart: statistical analysis and visualization of functional profiles for genes and gene clusters
clusterProfiler-book
a complete reference book for clusterProfiler and its sub-packages
ctat-mutations
Mutation detection using GATK4 best practices and latest RNA editing filters resources. Works with both Hg38 and Hg19
Deep-Image-Analogy
A linux version support for multiple images as input, based on https://github.com/msracver/Deep-Image-Analogy/tree/linux
DeepLC
DeepLC: Retention time prediction for (modified) peptides using Deep Learning.
Denovo-Proteogenomics-Pipeline
Denovo Proteogeomics pipeline to identify clinically relevent novel variants from RNAseq and Proteomics data.
denovogui
Graphical user interface for de novo sequencing of tandem mass spectra
immunopeptidogenomics
Tools for harnessing RNA-seq data to discover cryptic peptides in the immunopeptidome by mass spectrometry
ms2rescore
Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
msSLASH
Spectral library searching tool based on locality sensitive hashing
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
RNAseq-workflow
A repository for setting up a RNAseq workflow
RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
searchgui
Highly adaptable common interface for proteomics search and de novo engines
tensorflow
Computation using data flow graphs for scalable machine learning
ThermoRawFileParser
Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono
warp
WDL Analysis Research Pipelines