multiomics

parashardhapola/scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

bigbio/proteomics-sample-metadata

The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

abdenlab/oxbow

Read specialized NGS formats as data frames in R, Python, and more.

pinellolab/pyrovelocity

𝒫robabilistic modeling of RNA velocity ⬱

CostaLab/scMEGA

scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference

cantinilab/scconfluence

A novel method for single-cell diagonal integration: scConfluence

huidongchen/simba

SIMBA: SIngle-cell eMBedding Along with features

bigbio/sdrf-pipelines

A repository to convert SDRF proteomics files into pipelines config files

futianfan/GenoCraft

GenoCraft: A Comprehensive, User-Friendly Web Platform for High-Throughput Omics Data Analysis and Visualization (https://arxiv.org/pdf/2312.14249)

raw-lab/mercat2

MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data

AAnzel/MOVIS

MOVIS: A Multi-Omics Software Solution for Multi-modal Time-Series Clustering, Embedding, and Visualizing Tasks, by Aleksandar Anžel, Dominik Heider, and Georges Hattab

segalmicrobiomelab/lung_cancer_microbiome

alok-ai-lab/DeepInsight3D_pkg

DeepInsight3D package to deal with multi-omics or multi-layered data

Cajun-data/nanoSPLITS

Github repository for nanoSPLITS manuscript data and R scripts

phys2/belki

Visual exploration of multi-dimensional proteomics data

raevskymichail/epi-impute

Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

shuzwang/P2_cochlea

It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.

tagtag/TDbasedUFE

This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction

daisybio/keypathwayminer-R

R package for de novo pathway enrichment using KeyPathwayMiner

ErickNavarroD/RAMEN

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

ikmb/iptoolkit

A pythonic library for analysing immunopeptidomic experiments

PKU-BDBA/HTML

Code for Highly Trustworthy Multimodal Learning (HTML) Method on Omics

prokischlab/omicsDiagnostics

This repository contains different scripts to automate and visualize analysis performed for the "Integration of proteomics with genomics and transcriptomics increases the diagnosis rate of Mendelian disorders"

Surabhivj/BraneMF

BraneMF: Integration of Biological Networks for Functional Analysis of Proteins

SylviaYZ/bios-611-project

Project analyzing multi-omics genomics data from a COVID-19 study.

YuxingLu613/MoTIF

Multi-omics Trustworthy Integration Framework (MoTIF)

Angione-Lab/Synechococcus7002-metabolic-modelling

Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002

ikernunezca/Medulloblastoma

Multilayer Network analysis of medulloblastoma patients

bioinfocz/ComplexHeatmap-intro

ComplexHeatmap introduction

lmangnier/Benchmark_Integration_Metagenomics_Metabolomics

This repo is related to our benchmark entitled: "Decoding the microbiome-metabolome Nexus: A Systematic Benchmark of Integrative Strategies". We provide code to integrate metagenomics and metabolomics data to answer a variety of questions: such as global associations, data summarization, individual associations and feature selection.

manojmw/MultiOmics-ExomeSeq-Phenotype

Main Repository for my MASTER'S THESIS PROJECT

OmicsDI/ddiR

An R package to access to Omics Discovery Index API

twang15/PlatoAcademy

Free thoughts live

u-brite/ReproCanAtlas

Identifying cancer-related signatures of endometrial and ovarian cancer to develop a reproductive cancer atlas.

zhou-1314/Garfield

Graph-based Contrastive Learning enable Fast Single-Cell Embedding