gene-expression-profiles

There are 3 repositories under gene-expression-profiles topic.

seandavi / awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
analysis analysis-pipeline atac-seq awesome-list bioinformatics cell-clusters cell-cycle cell-differentiation cell-populations clustering data-integration data-visualization dimensionality-reduction gene-expression gene-expression-profiles python rna-seq-data rna-seq-experiments scrna-seq-data single-cell
3023
federicomarini / awesome-expression-browser
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
gene-expression rna-seq-data expression-browser bioinformatics awesome-list gene-expression-profiles atlas humancellatlas data-visualization data-exploration
126
tlatkowski / deep-learning-gene-expression
Deep learning methods for feature selection in gene expression autism data.
gene-expression autism neural-network deep-learning feature-selection autism-data gene-expression-profiles gene-annotation feature-extraction feature-detection features-extraction ttest microarray-data ncbi-database annotated-genes fisher-score python3 numpy data-mining google-colab
Language:Jupyter Notebook 32
TissUUmapsCore
TissUUmaps / TissUUmapsCore
TissUUmaps is a browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used as a web service or locally in your computer, and allows users to share regions of interest and local statistics.
bioinformatics computational biology gene-expression gene-expression-profiles digital-pathology
Language:JavaScript 20
maclean-lab / RVAgene
Recurrent Variational Auto gene encoder
gene-expression-profiles vae rnn scrna-seq-analysis
Language:Jupyter Notebook 19
novasmedley / deepRadiogenomics
Methods for training and interpreting deep radiogenomic neural networks
neural-networks imaging-genomics radiogenonmics glioblastoma gene-expression-profiles autoencoder
Language:Python 12
tbrunetti / NMF_unsupervised_clustering
Non-Negative Matrix Factorization for Gene Expression Clustering
nmf gene-expression-profiles unsupervised-learning clustering nonnegative-matrix-factorization clustering-algorithm clustering-methods kullback-leibler-divergence euclidean-distances gene-expression-signatures
Language:Python 7
kullrich / orthomap
orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.
orthofinder phylostratigraphy scanpy scrna-seq-analysis evolution expression-profiles gene-expression gene-expression-profiles bioinformatics orthomap python tai transcriptome
Language:Python 6
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
CoXPath / CoXPath
Scripts and data from "Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms"
bioinformatics disease-modeling gene-expression-profiles network-biology network-medicine pathway-analysis
Language:Jupyter Notebook 4
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
cashoes / sear
Simple (effin') Enrichment Analysis in R
enrichment-analysis pathway genomics transcriptomics gene-expression-profiles
Language:R 2
dccc-lab / AsthmaGXSigs
Shared TREM-1 expression signatures of asthma affection and control
enrichment-analysis gene-expression genomics gene-expression-signatures gene-expression-profiles r rstats asthma pathway-analysis published
Language:HTML 2
DEIB-GECO / GIS-weigthed_LASSO
Integrative approach to feature selection combining weighted LASSO and prior biological knowldge
classification feature-selection gene-expression-profiles lasso prior-knowledge
Language:Jupyter Notebook 2
krishan57gupta / ROSeq
ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. Takes in the complete filtered and normalized read count matrix, the location of the two sub-populations and the number of cores to be used.
tung vignette tung-dataset rank populations tutorial gene-expression-profiles gene-expression normalization tmm count-data
Language:R 2
kullrich / scTEI
add any phylogenetically based transcriptome evolutionary index (TEI) to single-cell data objects
seurat seurat-objects evolution expression-profiles gene-expression gene-expression-profiles orthofinder phylostratigraphy scrna-seq-analysis sctei bioinformatics
Language:HTML 2
cashoes / enumerateblood
A multi-response Gaussian model capable of accurately estimating the composition of blood samples from their gene expression profiles. Fit on Affymetrix Gene ST gene expression profiles using the glmnet R package.
deconvolution genomics transcriptomics glmnet composition blood-samples gene-expression-profiles
Language:R 1
GeneNetFusion
DEIB-GECO / GeneNetFusion
co-expression complex-networks gene-network-inference gene-expression-profiles network-fusion biomarkers
Language:Jupyter Notebook 1
krishan57gupta / iCTC
The goal of iCTC is to detect whether peripheral blood cells have CTCs (circulating tumor cell) or not.
circulating-tumor-cells ctc gene-expression gene-expression-profiles blood classification anomaly-detection pbmc cancer-genomics cancer-data jcm
Language:R 1
EcoGEx
sk-sahu / EcoGEx
Arabidopsis EcoGEx (R-📦 + 🕸️-App)
arabidopsis gene-expression gene-expression-profiles r r-package rpackage shiny-app shinyapp
Language:R 1
EliasFarr / SPOT
SPOT - Swift Profiling Of Transcriptomes - a shiny app for gene ranking according to user-defined expression profiles
transcriptomics shiny-apps expression gene-expression gene-expression-profiles gene-ranking differential-expression-analysis easy-to-use fast
Language:R 0
ImBenTremblay / CCSU_Special_Project_
Predicting the Probability or Occurrence of Relapse for Colorectal Cancer Patients using Gene Expression Data
cancer-genomics feature-selection gene-expression-profiles recursive-feature-elimination support-vector-machines random-forest classification data-science regression
0
krishan57gupta / ORsurv
survival of patients using ors on TCGA data
tcga-data survival patients ors gene-expression gene-expression-profiles molecule cells
Language:R 0
MarieOestreich / PRO-GENE-GEN
This repository contains the implementation for "Towards Biologically Plausible and Private Gene Expression Data Generation" (accepted at PoPETs 2024)
gene-expression-profiles generative-modeling privacy
Language:Jupyter Notebook 0
rajewsky-lab / SPACEGERM
SPACEGERM shiny app (archived, see GitLab for active fork)
shiny-apps gene-expression-profiles virtual-in-situ-hybridization spatial-clustering
Language:R 0
WojciechMigda / TCO-CMap2
CMap2 Top Coder Data Science Marathon Match
simd-parallelism multithreading gene-expression-profiles precision-medicine top-coder broad-institute nih weighted-kolmogorov-smirnov
Language:C++ 0
JDRomano2 / gexpro
A library and toolkit for common representation and analysis of gene expression profile data
computational-biology gene-expression-profiles gene-expression-signatures deep-learning library
Language:C++
RRafiee / GeneExpressionClassification
NanoString classifier based on NGS training set
nanostring ngs next-generation-sequencing normalization support-vector-machines classification classifier probability gene-expression-profiles gene-expression
Language:R