gene-expression

There are 17 repositories under gene-expression topic.

seandavi / awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
rna-seq-data gene-expression scrna-seq-data bioinformatics awesome-list dimensionality-reduction cell-cycle atac-seq analysis cell-differentiation python clustering cell-populations gene-expression-profiles rna-seq-experiments cell-clusters analysis-pipeline data-integration data-visualization single-cell
2898
COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
10x bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq sailfish salmon scrna-seq selective-alignment single-cell single-cell-rna-seq transcriptome
Language:C++ 727
saeyslab / nichenetr
NicheNet: predict active ligand-target links between interacting cells
single-cell-omics intercellular-communication ligand-receptor ligand-target data-integration single-cell-rna-seq rna-seq gene-expression network-inference cell-cell-communication
Language:R 437
lucidrains / enformer-pytorch
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
artificial-intelligence deep-learning gene-expression attention-mechanism transformer dna-sequences genomics
Language:Python 383
broadinstitute / Tangram
Spatial alignment of single cell transcriptomic data.
spatial-data visium gene-expression scrna-seq snrna-seq computational-biology
Language:Jupyter Notebook 219
iSEE / iSEE
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
clustering dimension-reduction feature-extraction gene-expression gui hacktoberfest human-cell-atlas shiny single-cell transcriptomics visualization
Language:R 217
junjunlab / ClusterGVis
One-step to Cluster and Visualize Gene Expression Matrix
mfuzz complexheatmap gene-clustering gene-expression visualization
Language:R 171
greenelab / tybalt
Training and evaluating a variational autoencoder for pan-cancer gene expression data
cancer-genomics deep-learning unsupervised-learning gene-expression variational-autoencoder script tool analysis autoencoder variational-autoencoders cancer
Language:HTML 157
uci-cbcl / D-GEX
Deep learning for gene expression inference
deep-learning gene-expression
Language:Python 144
fbrundu / pymrmr
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
feature-selection computational-biology data-science mutual-information gene-expression
Language:C++ 139
federicomarini / awesome-expression-browser
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
atlas awesome-list bioinformatics data-exploration data-visualization expression-browser gene-expression gene-expression-profiles humancellatlas rna-seq-data
123
saezlab / dorothea
R package to access DoRothEA's regulons
gene-expression tf-activities functional-analysis bioconductor-package transcription-factor regulons
Language:R 119
greenelab / pancancer
Building classifiers using cancer transcriptomes across 33 different cancer-types
tcga classifier transcriptome pancancer cancer gene-expression machine-learning methodology tool analysis
Language:Jupyter Notebook 117
bvieth / powsimR
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
gene-expression single-cell rna-seq simulation-framework simulation power experimental-design power-analysis r
Language:HTML 104
catavallejos / BASiCS
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
bayesian bioconductor-package gene-expression r rcpp rcpparmadillo scrna-seq single-cell
Language:R 83
nunofonseca / irap
integrated RNA-seq Analysis Pipeline
bulk-rna-seq differential-expression exon-quantification gene-expression irap pipeline rna-seq rna-seq-analysis single-cell-rna-seq transcript-quantification
Language:R 82
lucidrains / tf-bind-transformer
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
artificial-intelligence attention-mechanism deep-learning gene-expression transcription-factor-binding transcription-factors transformers
Language:Python 76
federicomarini / GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
rna-seq-data rna-seq-analysis transcriptomics r shiny transcriptome reproducible-research gui user-friendly bioconductor bioconductor-package functional-enrichment-analysis pathway-analysis gene-expression data-visualization data-exploration
Language:R 75
GfellerLab / EPIC
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
cancer-cells gene-expression bulk-data rna-seq cell-type
Language:R 69
aertslab / SCope
Fast visualization tool for large-scale and high dimensional single-cell data
single-cell large-scale-data-visualization gene-expression gene-regulatory-network aws cloud loom reactjs grpc
Language:Python 68
greenelab / adage
Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016
manuscript methodology research paper data supplement dataset machine-learning denoising-autoencoders neural-networks autoencoders gene-expression pseudomonas-aeruginosa
Language:Python 62
greenelab / BioBombe
BioBombe: Sequentially compressed gene expression features enhances biological signatures
gene-sets msigdb gene-expression tcga compression hetnet biobombe network autoencoder
Language:Jupyter Notebook 61
AAlhendi1707 / countToFPKM
Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)
gene-expression normalization rna-seq
Language:R 57
COMBINE-lab / terminus
rna-seq transcriptomics gene-expression
Language:Rust 55
JEFworks-Lab / MERINGUE
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
cell-cell-communication gene-expression rstats single-cell spatial-analysis spatial-transcriptomics
Language:R 50
uc-bd2k / GREIN
GREIN : GEO RNA-seq Experiments Interactive Navigator
rna-seq geo bioinformatics-pipeline bioinformatics-analysis rna-seq-pipeline rna-seq-data rna-seq-analysis graphical-interface r shiny-apps gene-expression-omnibus interactive-visualizations interactive-analysis processing geo-data-processing grein gene-expression
Language:HTML 47
andymckenzie / DGCA
Differential Gene Correlation Analysis
correlation r cran rna-seq differential-correlation gene-expression
Language:R 44
pinellolab / haystack_bio
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
epigenomics gene regulation tfs transcription-factor-binding rna-seq chip-seq fimo motifs epigenetics plasticity cell encode roadmap haystack-bio specific-regions haystack-pipeline gene-expression motif hotspot
Language:HTML 43
jasdumas / shinyGEO
Gene Expression Omnibus Analysis with Shiny :microscope:
bioinformatics data-visualization gene-expression r shiny
Language:CSS 39
SUwonglab / PECA
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
atac-seq chromatin-accessibiity dnase-seq gene-expression gene-regulatory-network rna-seq
Language:MATLAB 39
ezgisubasi / breast-cancer-gene-expression
This project aims to predict people who will survive breast cancer using machine learning models with the help of clinical data and gene expression profiles of the patients.
breast-cancer breast-cancer-classification gene-expression data-analysis data-visualization machine-learning
Language:Jupyter Notebook 38
drostlab / myTAI
Evolutionary Transcriptomics with R
evolutionary-transcriptomics r transcriptome evolution evo-devo studies-transcriptomes biological-processes gene-sets mytai gene-expression conservation expression-profiles
Language:R 35
randel / MixRF
A random-forest-based approach for imputing clustered incomplete data
random-forest gene-expression imputation mixed-models
Language:R 34
kieranrcampbell / clonealign
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
cancer-genomics gene-expression single-cell
Language:R 33
nuno-agostinho / psichomics
Interactive R package to quantify, analyse and visualise alternative splicing
splicing-quantification data-analyses alternative-splicing tcga differential-splicing-analysis gtex survival bioconductor sra recount2 differential-gene-expression gene-expression rna-seq-data vast-tools
Language:R 33
gaolabtools / scNanoGPS
Single cell Nanopore sequencing data for Genotype and Phenotype
cell-barcode demultiplexing gene-expression isoforms long-read-sequencing nanopore-analysis-pipeline rna-seq-pipeline single-cell single-nucleotide-variation umi-curation
Language:Python 32