bioinformatic-analysis Goto Github PK

bostongene

consensusml

Machine Learning to Detect Cancer Biomarkers from RNAseq Data

consensustme

covid19

dmp

Codes and sample data supporting the Dutch Microbiome Project. The preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.11.27.401125v1 and full data can be requested from EGA (https://ega-archive.org/studies/EGAS00001005027) and Lifelines biobank (https://www.lifelines.nl/researcher)

enrichment-analysis

R codes I uam using for getting from RNA-seq raw count to Pathways

epimesen-immunefilteration

Immune infiltration in cancer tissues: epithelial to mesenchymal transition

escc_time

Tumor Immune MicroEnvironment (TIME) of Esophageal Squamous Cell Carcinoma (ESCC)

fio-m6a-immune

Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma

genomederiveddiagnosis

identification-of-prognostic-related-genes-of-tme-derived-from-esca

Identification of prognostic related genes of tumor microenvironment derived from esophageal cancer patients

immucc

Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.

immune-infiltration

R codes for data analysis and visualization in immune infiltration

imsig

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours

interleukin-17-and-cytokine-related-signalings-are-determinants-for-tumor-immune-microenvironment-in

Interleukin-17 and cytokine-related signalings are determinants for tumor immune microenvironment in triple-negative breast cancer: in silico integrated analysis

iobr

IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.

istmescore

Calculation of immune and stromal scores in tumor microenvironment

lmqcm

R package lmQCM: An Algorithm for Gene Co-Expression Analysis

m6a

Methylation pattern mediated by m6A regulator and tumor microenvironment invasion in lung adenocarcinoma

mnp_training

DNA methylation-based classification of central nervous system tumours

modeling-iron-pathways-in-the-tumor-microenvironment

Predict regulatory components and model iron pathways in the tumor microenvironment

my_wgcna

nasopharyngeal-carcinoma

M6A-mediated molecular patterns and tumor microenvironment infiltration characterization in nasopharyngeal carcinoma

neoadjuvant-therapy-response-predictor

nmdcyt

R source code, outputs, and datasets for NMD-cytolytic immune infiltration paper (Zhao and Pritchard, PLoS Compt Biol, 2019)

nmibc_immuno-prognostic

This repository is built to reproduce all the statistical analyses and figures in the article entitled "A Robust Immuno-Prognostic Model of Non-muscle-invasive Bladder Cancer Indicates Dynamic Interaction in Tumor Immune Microenvironment Contributes to Cancer Progression".

ritmic

R package for studying the RegulatIon of Tumor MIcroenvironment Composition

tcga_brca

tmescore

Calculating Tumor microenvironment score

tmexplorer

A collection of tumour microenvironment single-cell RNA sequencing datasets for use in R and other pipelines.