glasgowcompbio/pyMultiOmics

Python toolbox for multi-omics data mapping and analysis

Language: Jupyter Notebook - Size: 45.9 MB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 15 - Forks: 4

ncaptier/stabilized-ica

This repository proposes a python implementation of a stabilized ICA algorithm

Language: Python - Size: 61.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 18 - Forks: 4

yollct/spycone

Spicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data

Language: Python - Size: 93.9 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 7 - Forks: 0

nf-core/tfactivity

Bioinformatics pipeline that makes use of expression and open chromatin data to identify differentially active transcription factors across conditions.

Language: Nextflow - Size: 5.07 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 6 - Forks: 0

meringlab/annotation_system_assessment

Snakemake pipeline to benchmark 11 functional pathway annotation systems

Language: Python - Size: 7.1 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

slipnitskaya/regulAS

regulAS: A Bioinformatics Tool for the Integrative Analysis of Alternative Splicing Regulome using RNA-Seq data

Language: Python - Size: 609 KB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

chengfgao/TopicVelo

TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems

Language: Jupyter Notebook - Size: 8.09 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 12 - Forks: 2

tnaake/MatrixQCvis

Language: R - Size: 4.47 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 1

cantinilab/HuMMuS

Molecular interactions inference from single-cell multi-omics data

Language: Python - Size: 78.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 13 - Forks: 3

pachterlab/voyager

From geospatial to spatial -omics

Language: R - Size: 4.1 GB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 60 - Forks: 6

babessell1/MADRID Fork of HelikarLab/COMO

Metabolic Drug Repurposing Pipeline

Language: Python - Size: 733 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 0

scverse/anndata

Annotated data.

Language: Python - Size: 4.33 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 501 - Forks: 150

danilotat/RNA-neoflow

Snakemake workflow to profile MHC-I neoepitopes with bulk tumor RNAseq data

Language: Python - Size: 211 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1

anergictcell/atg

A Rust library and CLI tool to handle genomic transcripts

Language: Rust - Size: 458 KB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 4 - Forks: 0

zhichaoxu04/MetaR2M

A novel meta-analysis framework of the R-squared (R2)-based mediation effect estimation for high-dimensional omics mediators

Language: R - Size: 1.27 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

rajewsky-lab/openst

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Language: HTML - Size: 170 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 25 - Forks: 7

owkin/PyDESeq2

A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

Language: Python - Size: 1.29 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 508 - Forks: 55

MartinLoza/Canek

Unbiased integration of single cell transcriptomes.

Language: R - Size: 38.4 MB - Last synced: 28 days ago - Pushed: 5 months ago - Stars: 5 - Forks: 1

GoekeLab/sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Language: Jupyter Notebook - Size: 2.36 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 87 - Forks: 23

PiotrTymoszuk/htGLMNET

High Throughput Light Weight Regularized Regression Modeling for Molecular Data

Language: R - Size: 43.4 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

sdomanskyi/DigitalCellSorter

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

Language: Python - Size: 1020 MB - Last synced: 22 days ago - Pushed: about 3 years ago - Stars: 22 - Forks: 10

mariachiaragrieco/bulk-RNAseq

bulk-RNAseq analysis for Transcriptomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: HTML - Size: 5.96 MB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

mariachiaragrieco/sc-RNAseq-colon

sc-RNAseq analysis for Transcriptomics Course 2021 (MSc Bioinformatics for Computational Genomics)

Size: 18.8 MB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

AliSajid/QTExpTool

What the Package Does (Title Case)

Language: R - Size: 570 KB - Last synced: 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

dohlee/chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Language: Python - Size: 137 MB - Last synced: 26 days ago - Pushed: 10 months ago - Stars: 29 - Forks: 0

benben-miao/TOmicsVis

Transcriptomics Visualization R package.

Language: R - Size: 198 MB - Last synced: about 18 hours ago - Pushed: 5 months ago - Stars: 56 - Forks: 11

spacetx/starfish

starfish: unified pipelines for image-based transcriptomics

Language: Python - Size: 114 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 220 - Forks: 66

LieberInstitute/deconvo_lute-paper

Contains analysis for the lute software paper

Language: HTML - Size: 541 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

becavin-lab/bacnet

BACNET is a Java based platform to develop website for multi-omics analysis

Language: Java - Size: 148 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 13 - Forks: 1

Novartis/cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.

Language: Python - Size: 203 KB - Last synced: 26 days ago - Pushed: 3 months ago - Stars: 52 - Forks: 32

iSEE/iSEE_custom

Examples of custom panels for the iSEE package

Language: R - Size: 3.41 MB - Last synced: about 1 month ago - Pushed: over 4 years ago - Stars: 6 - Forks: 1

urmi-21/MetaOmGraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Language: Java - Size: 175 MB - Last synced: 2 months ago - Pushed: about 2 years ago - Stars: 32 - Forks: 14

DeplanckeLab/ASAP

ASAP : Automated Single-cell Analysis Pipeline

Language: Java - Size: 170 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 23 - Forks: 10

thelovelab/fishpond

Differential expression and allelic analysis, nonparametric statistics

Language: R - Size: 7.01 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 24 - Forks: 9

C4TB/shinyExprPortal

Deploy interactive Shiny portals for exploration and showcase of analysis of molecular expression and phenotype data using a configuration file.

Language: R - Size: 7.64 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 4 - Forks: 1

almeidasilvaf/bears

An R package to create gene expression atlases from bulk RNA-seq data on NCBI SRA

Language: R - Size: 5.17 MB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 2 - Forks: 0

almeidasilvaf/HybridExpress_paper

Data and code associated with the paper "HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors"

Language: JavaScript - Size: 11.4 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

czbiohub-sf/tabula-sapiens

Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens

Language: Jupyter Notebook - Size: 788 MB - Last synced: 26 days ago - Pushed: about 1 year ago - Stars: 37 - Forks: 7

pietrocinaglia/fape

Flexible Automated Pipeline Engine (FAPE)

Size: 7.93 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

colbyford/zebrafish_mecp2_expression

Behavioral and Transcriptomic Analyses of mecp2 Function in Zebrafish

Language: HTML - Size: 120 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 3 - Forks: 0

Neal-Liu1/Multi-omics-integration

Contains code related to my multi-omics integration project at WEHI.

Language: R - Size: 136 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

gogleva/ShinyTranscriptomes

project for Cambridge Bioinformatics Hackathon, 25-27 Sept 2017

Language: R - Size: 895 KB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

gogleva/PublicPalmivora

Reproducible scripts for (P. Carella et al) manuscript

Language: R - Size: 1.67 MB - Last synced: 3 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

pallavisurana1/TransTEx

R package for TransTEx: Novel tissue-specificity scoring method for grouping human transcriptome in-to different expression groups

Language: R - Size: 18.6 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

lvn3668/caBIO-load-scripts

ETL scripts to populate caBIO database

Size: 26.7 MB - Last synced: 3 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

snail123815/oleveler

This is mirror repository of https://gitlab.services.universiteitleiden.nl/duc/oleveler

Language: Python - Size: 10.8 MB - Last synced: 3 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

Sydney-Informatics-Hub/Bioinformatics

A suite of bioinformatics data processing and analysis pipelines, software, and training resources for common DNA and RNA sequence analysis methods.

Size: 137 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 11 - Forks: 0

lcalviell/Ribo-seQC

A comprehensive analysis tool for Ribo-seq and small RNA-seq data

Language: HTML - Size: 16.1 MB - Last synced: 3 months ago - Pushed: almost 4 years ago - Stars: 8 - Forks: 5

GoekeLab/xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

Language: Python - Size: 4.96 MB - Last synced: 29 days ago - Pushed: about 1 month ago - Stars: 127 - Forks: 22

StatBiomed/UniTVelo

UniTVelo, Temporally Unified RNA Velocity for single cell trajectory inference

Language: Jupyter Notebook - Size: 20.2 MB - Last synced: 3 months ago - Pushed: 10 months ago - Stars: 22 - Forks: 9

zavolanlab/zarp

The Zavolab Automated RNA-seq Pipeline

Language: Python - Size: 23.8 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 28 - Forks: 5

krassowski/gsea-api

Pandas API for multiple Gene Set Enrichment Analysis implementations in Python (GSEApy, cudaGSEA, GSEA)

Language: Python - Size: 162 KB - Last synced: about 1 month ago - Pushed: about 1 year ago - Stars: 14 - Forks: 2

parashardhapola/nabo

Python library to perform memory efficient cross-sample cell mapping using single cell transciptomics (scRNA-Seq) data

Language: Python - Size: 3.38 MB - Last synced: 22 days ago - Pushed: over 3 years ago - Stars: 3 - Forks: 3

guigolab/LyRic

Long RNA-seq analysis workflow

Language: Python - Size: 664 KB - Last synced: 27 days ago - Pushed: 27 days ago - Stars: 10 - Forks: 4

bpucker/Boas_Pucker

Homepage of Boas Pucker listing publications and professional activities

Size: 101 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 0

louadi/NEASE

A network-based approach for exon set enrichment

Language: Python - Size: 49.3 MB - Last synced: 24 days ago - Pushed: about 2 months ago - Stars: 12 - Forks: 2

PaulaRS/snakemake_transcriptome_workflow

Reusable workflow for de novo transcriptome assemblies from paired-end illumina reads, annotation and quality checks

Language: CAP CDS - Size: 182 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

jlchen5/gene2protein

Predicting the protein level with gene expression

Language: Python - Size: 10.7 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

zavolanlab/zarp-cli

A user-friendly command-line interface for the ZARP RNA-seq analysis workflow

Language: Python - Size: 42.8 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 1

sales-lab/spatialDE

R wrapper for SpatialDE

Language: R - Size: 1.46 MB - Last synced: 29 days ago - Pushed: 4 months ago - Stars: 3 - Forks: 3

AllenInstitute/scrattch.vis

scRNA-seq data visualization from scrattch

Language: R - Size: 104 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 22 - Forks: 2

eudoraleer/scasa

SCASA: Single cell transcript quantification tool

Language: R - Size: 27.9 MB - Last synced: 3 months ago - Pushed: 7 months ago - Stars: 16 - Forks: 4

Louise-la/RNA_seq_alignment_pipeline

RNA-Seq Pipeline for processing paired-end FASTQ transcripts generated from Illumina sequencing. The pipeline trims adapter sequences, aligns transcripts to a specified region of interest on the reference genome, and facilitates downstream analysis.

Language: Python - Size: 13.7 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

COMBINE-lab/terminus

Language: Rust - Size: 406 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 55 - Forks: 3

fhaive/Curated-and-harmonised-transcriptomics-datasets-of-interstitial-lung-disease-patients

Curated and harmonised transcriptomics datasets of interstitial lung disease patients

Language: R - Size: 82 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Oshlack/MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

Language: Python - Size: 21.8 MB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 32 - Forks: 7

michalbukowski/dge-ontology

Jupyter notebooks for DGE results and ontology analysis and visualisation.

Language: Jupyter Notebook - Size: 1.09 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

Nuwa-genomics/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 431 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

AstraBert/SacCerML

SacCerML is a machine-learning classifier that enables gene calling for Saccharomyces cerevisiae FASTA sequences

Language: Jupyter Notebook - Size: 4.93 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

dieterich-lab/nmdtxdb

Shiny application and code for the database for NMD targets

Language: R - Size: 112 MB - Last synced: 3 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

markziemann/dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Language: Shell - Size: 56 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 39 - Forks: 8

nanoporetech/isONclust2

A tool for de novo clustering of long transcriptomic reads

Language: C++ - Size: 643 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 13 - Forks: 3

SimonHegele/Ivoforms

A package dedicated to the simulation of sequencing read data corresponding to randomly generated genes with predifined splice-models for the evaluation of transcriptome assembly tools

Language: Jupyter Notebook - Size: 118 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

galantelab/sandy

A straightforward and complete next-generation sequencing read simulator

Language: Perl - Size: 25.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 15 - Forks: 2

CABSEL/DeltaFBA

DeltaFBA is a set of MATLAB functions that employs constraint-based modeling, in combination with differential gene expression data, to evaluate changes in the intracellular flux distribution between two conditions.

Language: MATLAB - Size: 894 MB - Last synced: 3 months ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 1

leandrotiburske/BipolarDisorder

Transcriptome analysis from patients with Bipolar Affective Disorder

Language: R - Size: 68.4 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

kalilamali/ucm_genomes_and_genome_analysis

R code in R Markdown used for ucm genomes and genome analysis course

Language: HTML - Size: 61.6 MB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 170 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 37 - Forks: 11

denniswiersma/internship

Code and writings for my internship project at the Transcriptomic Bioinformatics research group at University Medical Center Groningen.

Language: Jupyter Notebook - Size: 6.42 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

cashoes/sear

Simple (effin') Enrichment Analysis in R

Language: R - Size: 91.6 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 0

julianneyang/transcriptomicsonhoffman

Walks through installation and usage of FASTQC, MultiQC, Trimmomatic, and Salmon for transcriptomic data preprocessing. Includes Grid Engine shell scripts that can be looped over many files in a directory.

Language: R - Size: 20.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

transbioZI/BioMM

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Language: HTML - Size: 12.2 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 14 - Forks: 1

OpenOmics/modr

An awesome Oxford Nanopore Pipeline for direct RNA-sequencing

Language: Python - Size: 689 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 1

robogeno/SVMDO

Shiny Interactive Web App for Extracting Disease-Associated Discriminative Gene Set from RNA-Seq Cancer Transcriptomic Datasets

Language: R - Size: 8.25 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

mehdimunim/GUI_for_RNA_seq

Graphical User Interface using Shiny for RNA-seq analysis

Language: R - Size: 3.96 MB - Last synced: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

OlivierRaineteauSBRI/scRNASeq

Repo linked to our recent publication in Science Advances

Language: HTML - Size: 5.66 GB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

tracykuper/mimics

Multi-scale model of Metabolism In Cellular Systems

Language: Java - Size: 8.66 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

JulienMoehlin/MULTILAYER_Docker

Multilayer on Docker. Spatial transcriptomics analysis tool (Spatial biology).

Language: Python - Size: 1.5 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

skr1/Imagene

ImaGene: A multi-omic ML/AI software with guided operational reports and supporting files

Language: HTML - Size: 50.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 5 - Forks: 3

pblumenkamp/Curare

Curare - A customizable and reproducible analysis pipeline for RNA-Seq experiments

Language: Python - Size: 47.3 MB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 7 - Forks: 1

nlawlor/V-SVA

V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data

Language: R - Size: 22.8 MB - Last synced: 3 months ago - Pushed: over 4 years ago - Stars: 7 - Forks: 3

klarman-cell-observatory/scPlot

Single cell interactive plotting tools

Language: Jupyter Notebook - Size: 37.9 MB - Last synced: 1 day ago - Pushed: almost 4 years ago - Stars: 24 - Forks: 8

TCP-Lab/bioTEA

bioTEA - A user friendly tool to perform transcript expression analysis

Language: Python - Size: 15.6 MB - Last synced: 6 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 2

stracquadaniolab/cubseq-nf

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

Language: R - Size: 187 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

Bayer-Group/cellenium

Cellenium is a FAIR and scalable interactive visual analytics app for scRNA-Seq data (single-cell RNA sequencing).

Language: Jupyter Notebook - Size: 12.4 MB - Last synced: about 2 months ago - Pushed: 7 months ago - Stars: 23 - Forks: 4

dib-lab/dammit

just annotate it, dammit!

Language: Python - Size: 12.1 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 87 - Forks: 28

Iwo-K/genespector

Language: Python - Size: 4.65 MB - Last synced: 6 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1

BPDanek/multi-omics-pdd-FL-study

Federated Learning for multi-omics: a performance evaluation in Parkinson’s disease by Benjamin Danek, Mary B. Makarious, Anant Dadu, Dan Vitale, Paul Suhwan Lee, Mike A Nalls, Jimeng Sun, Faraz Faghri

Language: Jupyter Notebook - Size: 5.6 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 2 - Forks: 1

OmicsSuite/OmicsSuite.github.io

OmicsSuite website for releasing new version.

Language: HTML - Size: 14.8 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 15 - Forks: 1

delosh653/ECHO

An application to find and visualize circadian rhythms in time course data using extended harmonic oscillators.

Language: R - Size: 6.86 MB - Last synced: 4 months ago - Pushed: almost 4 years ago - Stars: 12 - Forks: 0