chjp's Stars
geekywrites/datascience
This repository is a compilation of free resources for learning Data Science.
gokceneraslan/awesome-deepbio
A curated list of awesome deep learning applications in the field of computational biology
stephenturner/oneliners
Useful bash one-liners for bioinformatics.
saeyslab/nichenetr
NicheNet: predict active ligand-target links between interacting cells
jmzeng1314/scRNA_smart_seq2
abidlabs/deep-learning-genomics-primer
Contains files for the deep learning in genomics primer.
NBISweden/excelerate-scRNAseq
Single RNA-seq data analysis with R (Finland, May, 2019)
dpeerlab/Palantir
Single cell trajectory detection
tabdelaal/scRNAseq_Benchmark
Bench-marking classification tools for scRNA-seq data
AlexandrovLab/SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
harvardinformatics/bioinformatics-coffee-hour
Short lessons from FAS Informatics coffee hour
czbiohub-sf/tabula-muris-senis
Tabula Muris Senis
niu-lab/msisensor2
Microsatellite instability (MSI) detection for tumor only data.
bioinfo-ibms-pumc/SCSA
SCSA: cell type annotation for single-cell RNA-seq data
ParkinsonLab/Metatranscriptome-Workshop
Metatranscriptomics Tutorial
rhshah/IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
zellerlab/crc_meta
Code and analysis results for the CRC shotgun meta-analysis
ShixiangWang/Variants2Neoantigen
A neoantigen calling pipeline begins from variants record file (MAF) (Not maintain now)
dhbradshaw/ml-for-genomics
Lists open source machine learning projects solving genomic or molecular biology problems.
pogorely/ALICE
Detecting TCR involved in immune responses from single RepSeq datasets
bioinformatics-core-shared-training/CRUK_CI_RNAseq_course
Base CRUK Cambridge Institute RNAseq Course
umccr/umccrise
:snake: DRAGEN Tumor/Normal workflow post-processing
Hughes-Genome-Group/deepHaem
Implementation of a deep convolutional neural network for predicting chromatin features from DNA sequence
PascaDiMagliano-Lab/MultimodalMappingPDA-scRNASeq
Raw data and analysis of scRNA Seq experiments for the paper Multimodal Mapping of the Immune Landscape in Human Pancreatic Cancer. This repository includes the raw data and core R script that will replicate Figures 1E, 1G, 1H, and Supplementary Figure 1D. To replicate the analysis, place the R script in R Studio and load the data into the Global Environment. The R script will then run and generate the four figures found in the manuscript. Veerin Sirihorachai July 31, 2019
gerstung-lab/signature-interactions
Mutational signatures are jointly shaped by DNA damage and repair
mitlovelab/SeqWell-TCR
Supplementary information, scripts, and protocols related to Tu A., et al. Nat. Immunol. 2019
ruthanium/antigen-combos-scripts
Discriminatory power of combinatorial antigen recognition in cancer T cell therapies
MarioniLab/Tumorigenesis2018
team113sanger/mouse-mutatation-signatures
This repository contains the code for the paper "The mutational signature profile of known and suspected human carcinogens in mice"
jsevo/wbcdynamics_microbiome
Analysis code relating bacterial microbiota compositions to white blood cell dynamics during immune reconstitution.