multiomics

There are 2 repositories under multiomics topic.

theislab / scarches
Reference mapping for single-cell genomics
single-cell deep-learning rna-seq-analysis data-integration batch-correction multimodal-deep-learning multiomics single-cell-genomics scrna-seq human-cell-atlas
Language:Jupyter Notebook 328
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.
big-data bioinformatics cite-seq clustering differential-expression dimension-reduction gene-modules genomics graph-analytics memory-efficient multiomics pseudotime scalable-data-analysis scatac-seq scrna-seq single-cell-atac-seq single-cell-genomics single-cell-rna-seq tsne umap
Language:Python 92
bigbio / proteomics-sample-metadata
The Proteomics Experimental Design file format: Standard for experimental design annotation
metadata sdrf pride-metadata proteomics msrun-metadata multiomics sdrf-proteomics proteomics-datasets proteomics-community proteomics-experiments proteomexchange mage-tab
Language:Python 75
abdenlab / oxbow
Read specialized NGS formats as data frames in R, Python, and more.
apache-arrow bioinformatics data-science dataframe fair-data genomics multiomics ngs pandas polars python r rust-lang
Language:Rust 58
pyrovelocity
pinellolab / pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming rna-velocity rna-velocity-estimation single-cell-genomics single-cell-rna-seq transcriptomics rna-splicing rna-splicing-analysis single-cell-multiomics pyro
Language:Python 40
CostaLab / scMEGA
scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
grn single-cell multiomics
Language:R 34
bigbio / sdrf-pipelines
A repository to convert SDRF proteomics files into pipelines config files
multiomics msstats sdrf proteomics-data-analysis proteomics mass-spectrometry
Language:Python 16
huidongchen / simba
SIMBA: SIngle-cell eMBedding Along with features
graph-embedding multiomics single-cell-analysis dimensionality-reduction embedding graph
Language:Python 16
raw-lab / mercat2
MerCat2: python code for versatile k-mer counting and diversity estimation for database independent property analysis for metaome data
python diversity plotly multiomics multiomics-data protein dask fastq k-mer-counting k-mer-frequency divideandconquer metagenomic-analysis metatranscriptomic-analysis kmer-frequency-count nucleotides diversity-estimation database-independent-analysis
Language:HTML 11
cantinilab / scconfluence
A novel method for single-cell diagonal integration: scConfluence
dimension-reduction integration multiomics optimal-transport single-cell
Language:Python 10
MOVIS
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
multiomics multiomics-data visualization clustering machine-learning bioinformatics time-series time-series-analysis exploratory-data-analysis cross-platform web-app
Language:Python 9
segalmicrobiomelab / lung_cancer_microbiome
microbiome multiomics transcriptome 16s-rrna 16s rna-seq rna-seq-analysis
Language:R 8
alok-ai-lab / DeepInsight3D_pkg
DeepInsight3D package to deal with multi-omics or multi-layered data
ai artificial-intelligence class-activation-maps classification cnn cnn-classification convolutional-neural-networks deep-learning deepfeature deepinsight gpu image machine-learning multiomics recognition tabular-data test training validation
Language:MATLAB 6
Cajun-data / nanoSPLITS
Github repository for nanoSPLITS manuscript data and R scripts
multiomics proteomics proteomics-data single-cell-omics
Language:HTML 5
phys2 / belki
Visual exploration of multi-dimensional proteomics data
proteomics multiomics data-visualization machine-learning
Language:C++ 5
raevskymichail / epi-impute
Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data
epigenetics imputation integration multiomics scatac-seq scrna single-cell chromatin
Language:R 5
shuzwang / P2_cochlea
It contains the functional code to analyze P2 scRNA-seq and scATAC-seq data.
single-cell-omics gene-regulatory-network multiomics cochlea scrna-seq scatac-seq
Language:R 5
tagtag / TDbasedUFE
This is a R package that intends to perform all the features possible by tensor decomposition based unsupervised feature extraction
bioinformatics dna-methylation gene-expression-profiles histone-modifications multiomics tensor-decomposition
Language:R 5
keypathwayminer-R
daisybio / keypathwayminer-R
R package for de novo pathway enrichment using KeyPathwayMiner
standalone pathway-enrichment-analysis interaction-network omics gene-expression-profiles de-novo-pahtway-enrichment singelcell biological-networks multiomics r r-package systems-biology
Language:R 4
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.
exposome genome methylation-analysis methylation-microarrays multiomics r-package bioinformatics-tool dna-methylation
Language:R 4
ikmb / iptoolkit
A pythonic library for analysing immunopeptidomic experiments
seaborn hla immunoinformatics immunopeptidomics bioinformatics multiomics plotly data-science
Language:Python 4
PKU-BDBA / HTML
Code for Highly Trustworthy Multimodal Learning (HTML) Method on Omics
dynamic-neural-network multimodal multiomics trustworthy-ai
Language:Python 4
omicsDiagnostics
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"
hpo multiomics proteomics rare-disease rna-seq diagnostics outlier-detection
Language:R 4
Surabhivj / BraneMF
BraneMF: Integration of Biological Networks for Functional Analysis of Proteins
bioinformatics systems-biology network-integration multiomics
Language:Python 4
SylviaYZ / bios-611-project
Project analyzing multi-omics genomics data from a COVID-19 study.
bioinformatics cite-seq multiomics scrna-seq covid-19
Language:R 4
Angione-Lab / Synechococcus7002-metabolic-modelling
Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002
machine-learning cyanobacteria flux-balance-analysis metabolic-network multiobjective-optimization multiomics
Language:MATLAB 3
ikernunezca / Medulloblastoma
Multilayer Network analysis of medulloblastoma patients
multilayer network rare-disease multiomics community-detection modularity trajectories
Language:R 3
YuxingLu613 / MoTIF
Multi-omics Trustworthy Integration Framework (MoTIF)
dynamic-neural-network multimodal multiomics trustworthy-ai
Language:Python 3
bioinfocz / ComplexHeatmap-intro
ComplexHeatmap introduction
complexheatmap heatmap bioinformatics bioconductor bioconductor-package rna-seq chip-seq atac-seq omics multiomics visualization gene-expression
Language:HTML 2
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.
inferential-statistics metabolomics metagenomics multiomics statistical-models
Language:R 2
manojmw / MultiOmics-ExomeSeq-Phenotype
Main Repository for my MASTER'S THESIS PROJECT
multiomics interactome exome-sequencing phenotype machine-learning clustering candidate-genes variants mendelian monogenic
Language:Python 2
OmicsDI / ddiR
An R package to access to Omics Discovery Index API
r rest-client omicsdi multiomics
Language:R 2
twang15 / PlatoAcademy
Free thoughts live
multiomics statistics machine-learning high-performance-computing bioinformatics medicine
2
u-brite / ReproCanAtlas
Identifying cancer-related signatures of endometrial and ovarian cancer to develop a reproductive cancer atlas.
biohackathon bioinformatics cancer endometrial-cancer hackin-omics-2022 multiomics signatures ubrite
Language:HTML 2
MendenLab / miRNAInt_Ferroptosis
Multi-omics differential expression and integration using PPI networks
differential-expression-analysis multiomics omics-data-integration protein-protein-interaction-network
Language:R 1
zqzneptune / ShinyCITExpresso
A ShinyApp for visualization and explorering Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data
cite-seq multiomics r shiny-apps
Language:R 1