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Search results for gene expression
gene-expression
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104 search results found
Awesome Single Cell
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2,784
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Salmon
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661
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Nichenetr
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416
NicheNet: predict active ligand-target links between interacting cells
Enformer Pytorch
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359
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
Isee
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217
R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Tangram
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153
Spatial alignment of single cell transcriptomic data.
Pymrmr
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135
Python3 binding to mRMR Feature Selection algorithm (currently not maintained)
D Gex
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117
Deep learning for gene expression inference
Clustergvis
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114
One-step to Cluster and Visualize Gene Expression Matrix
Awesome Expression Browser
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107
😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎
Tybalt
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107
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Dorothea
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105
R package to access DoRothEA's regulons
Powsimr
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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
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81
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
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74
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
Epic
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68
Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.
Pancancer
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61
Building classifiers using cancer transcriptomes across 33 different cancer-types
Irap
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58
integrated RNA-seq Analysis Pipeline
Scope
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56
Fast visualization tool for large-scale and high dimensional single-cell data
Tf Bind Transformer
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45
A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
Biobombe
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44
BioBombe: Sequentially compressed gene expression features enhances biological signatures
Terminus
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43
Dgca
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38
Differential Gene Correlation Analysis
Haystack_bio
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35
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Peca
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35
PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data
Shinygeo
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35
Gene Expression Omnibus Analysis with Shiny 🔬
Mytai
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33
Evolutionary Transcriptomics with R
Psichomics
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33
Interactive R package to quantify, analyse and visualise alternative splicing
Meringue
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33
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Grein
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30
GREIN : GEO RNA-seq Experiments Interactive Navigator
Rnaseq_titration_results
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29
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Cobrame
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29
A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Scnanogps
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29
Single cell Nanopore sequencing data for Genotype and Phenotype
Ouija
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29
Descriptive probabilistic marker gene approach to single-cell pseudotime inference
Volcano3d
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28
An R package to plot interactive three-way differential expression analysis
Bird
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27
Big data Regression for predicting DNase I hypersensitivity
Clonealign
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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
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24
This tutorial is created for educational purpose
Asap
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24
ASAP : Automated Single-cell Analysis Pipeline
Chromoformer
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24
The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
Go_enrichment
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23
Transcripts annotation and GO enrichment Fisher tests
Mixrf
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23
A random-forest-based approach for imputing clustered incomplete data
Fishpond
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23
Differential expression and allelic analysis, nonparametric statistics
Lincs
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20
Library of Integrated Cellular Signatures L1000
Gedfn
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19
GEDFN: Graph-Embedded Deep Feedforward Network
Rnaseq Pipeline
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18
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Microscope
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17
ChIP-seq/RNA-seq analysis software suite for gene expression heatmaps
Neuroexpresso
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16
📊 Gene expression in neuroexpresso database
Pipernaseq
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16
A comprehensive pipeline for RNAseq data analysis
Graphsim
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16
R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)
Switchde
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15
Inference of switch-like differential expression along single-cell trajectories
Glmmseq
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15
Gene-level general linear mixed model
Immucc
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15
Cell-Centric View of Tissue Transcriptome Measuring Cellular Compositions of Immune Microenvironment From Mouse RNA-Seq Data.
Vidger
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15
Make rapid visualizations of RNA-seq data in R
Glmmseq
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15
Gene-level general linear mixed model
Cancer Data
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14
TCGA data acquisition and processing for Project Cognoma
Diane
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13
Dashboard for the Inference and Analysis of Networks from Expression data
Gne
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13
This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"
Circompara
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12
🔬 A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Npdr
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12
NPDR: Nearest-neighbor Projected-Distance Regression with the generalized linear model
Tissuumapscore
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12
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.
Bretigea
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11
Brain Cell Type Specific Gene Expression Analysis
Scinsight
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11
Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data
Generic Expression Patterns
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11
Distinguishing between generic and experiment-specific gene expression signals.
Archive Ruvseq
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11
Archived version of RUVSeq
Netprophet_2.0
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11
A “data light” TF-network mapping algorithm using only gene expression and genome sequence data.
Deep Learning Gene Expression
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10
Deep learning methods for feature selection in gene expression autism data.
Icodon
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10
iCodon customizes gene expression based on the codon composition
Geneexpressionaging
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10
Gene expression viewer template
Mybmonday
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10
MYB transcription factors are one of the largest gene family in plants and control many processes. This repository provides additional background to the #MYB_Monday tweets
Raptor
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10
RAPToR (Real Age Prediction from Transcriptome staging on Reference) is a tool to accurately predict individual samples' developmental age from their gene expression profiles.
Gear
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10
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
Biomm
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9
BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data
Pancancer Evaluation
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9
Evaluating genome-wide prediction of driver mutations using pan-cancer data
Pyreqtl
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9
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.
Rna Seq Vae
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9
Synthetic gene expression data generation using Variational Auto-Encoder
Pinetree
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9
🌲 a flexible gene expression simulator with codon-specific translation rates
Hgsc_subtypes
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8
Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four
Bgee_pipeline
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8
Source code of the Bgee pipeline used to build the Bgee database
Genome_integration
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8
MR-link and genome integration. genome_integration is a repository for the analysis of genomic data. Specifically, the repository implements the causal inference method MR-link, as well as other Mendelian randomization methods.
Rna Seek
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8
A comprehensive quality-control and quantification RNA-seq pipeline
Gc Splem
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8
Survival Prediction for Gastric Cancer via Multimodal Learning of Whole Slide Images and Gene Expression -- BIBM 2022
Gbm_immune_validation
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8
Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors
Adversarial Gene Expression
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8
Adversarial generation of gene expression data using Generative Adversarial Networks
Resvae
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7
resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.
Fungiexpresz
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7
An R-shiny package to analyse and visualise fungal gene expression data
Flexgsea R
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7
Flexible gene set enrichment analysis
Sbmlme
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7
Encoding ME models in SBML
Pcmf
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7
pCMF R package
Tag Seq
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6
3’ Tag RNA-seq pipeline (Work in progress)
Refex
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6
RefEx: a reference gene expression dataset of mammalian tissues and cell lines measured by different methods
Knowseq
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6
KnowSeq R package
Pathcore T Analysis
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6
This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.
Java Genetic Programming
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6
Genetic-programming framework for various genetic programming paradigms such as linear genetic programming, tree genetic programming, gene expression programming, etc
Grex
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6
Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Orthomap
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6
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.
Survcomp
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6
R package for performance assessment and comparison for survival analysis
Cancer
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6
💹 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).
Moomin
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5
MOOMIN is a tool for analysing differential expression data
Metagx
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5
Scripts to perform meta-analysis of cancer gene expression datasets
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