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45 search results found

Nichenetr ⭐ 416

NicheNet: predict active ligand-target links between interacting cells

Clustergvis ⭐ 114

One-step to Cluster and Visualize Gene Expression Matrix

Dorothea ⭐ 105

R package to access DoRothEA's regulons

Powsimr ⭐ 102

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.

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

Genetonic ⭐ 74

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

integrated RNA-seq Analysis Pipeline

Differential Gene Correlation Analysis

Shinygeo ⭐ 35

Gene Expression Omnibus Analysis with Shiny 🔬

Evolutionary Transcriptomics with R

Meringue ⭐ 33

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

Psichomics ⭐ 33

Interactive R package to quantify, analyse and visualise alternative splicing

GREIN : GEO RNA-seq Experiments Interactive Navigator

Descriptive probabilistic marker gene approach to single-cell pseudotime inference

Clonealign ⭐ 25

Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data

Rna Seq Tutorial For Gene Differential Expression Analysis ⭐ 24

This tutorial is created for educational purpose

A random-forest-based approach for imputing clustered incomplete data

Microscope ⭐ 17

ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps

Neuroexpresso ⭐ 16

📊 Gene expression in neuroexpresso database

Graphsim ⭐ 16

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.

Gene-level general linear mixed model

Switchde ⭐ 15

Inference of switch-like differential expression along single-cell trajectories

Gene-level general linear mixed model

Make rapid visualizations of RNA-seq data in R

Dashboard for the Inference and Analysis of Networks from Expression data

Circompara ⭐ 12

🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data

NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model

Bretigea ⭐ 11

Brain Cell Type Specific Gene Expression Analysis

Netprophet_2.0 ⭐ 11

A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.

Archive Ruvseq ⭐ 11

Archived version of RUVSeq

iCodon customizes gene expression based on the codon composition

A collection of Python modules equivalent to R ReQTL Toolkit aims to identify the association between expressed SNVs with their gene expression using RNA-sequencing data.

Gbm_immune_validation ⭐ 8

Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors

Hgsc_subtypes ⭐ 8

Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four

Fungiexpresz ⭐ 7

An R-shiny package to analyse and visualise fungal gene expression data

Flexgsea R ⭐ 7

Flexible gene set enrichment analysis

3’ Tag RNA-seq pipeline (Work in progress)

RefEx: a reference gene expression dataset of mammalian tissues and cell lines measured by different methods

Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data

KnowSeq R package

💹 The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

Identification of candidate causal perturbations from differential gene expression data

Scripts to perform meta-analysis of cancer gene expression datasets

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