wuyank

flexbar

flexible barcode and adapter removal

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

neoepiscope

predicts neoepitopes from phased somatic mutations detected using tumor/normal DNA-seq data

MuPeXI

MuPeXI: the mutant peptide extractor and informer, a tool for predicting neo-epitopes from tumor sequencing data.

vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy

pVACtools

QBRC-Neoantigen-Pipeline

QBRC Neoantigen calling pipeline with CSiN calculation embedded

QBRC-Somatic-Pipeline

QBRC Somatic Mutation Calling Pipeline

PyTorch_Tutorial

《Pytorch模型训练实用教程》中配套代码

atmtcr

Attention-aware contrastive learning for TCR-antigen binding

TITAN

Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2021)

ImRex

Generic TCR-epitope recognition prediction using CNN approach on both known and novel epitopes

NetTCR-2.0

NetTCR-2.0. Sequence-based prediction of peptide-TCR binding

AttnTAP

An attention-fused BiLSTM model used to predict TCR-peptide binding accuracy.

DLpTCR

Predicting immunogenic peptide recognized by TCR through ensemble deep learning

pMTnet

Deep Learning the T Cell Receptor Binding Specificity of Neoantigen

ML2022-Spring

**Official** 李宏毅 (Hung-yi Lee) 機器學習 Machine Learning 2022 Spring

ProjecTILs

Interpretation of cell states using reference single-cell maps

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

CRISPResso2

Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments

InSiDeR

InSiDeR

EasyFuse

EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.

gatk4-jupyter-notebook-tutorials

This repository contains Jupyter Notebooks containing GATK Best Practices Workflows

gatk4-germline-snps-indels

Workflows for germline short variant discovery with GATK4

gatk4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools

seq-format-conversion

Workflows for converting between sequence data formats

gatk4-data-processing

Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools

RNA-seq

A BioWDL pipeline for processing RNA-seq data, starting with FASTQ files to produce expression measures and VCFs. Category:Multi-Sample

wdl

Workflow Description Language - Specification and Implementations

Trimmomatic