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26 search results found

Awesome Single Cell ⭐ 2,784

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

Awesome Expression Browser ⭐ 107

😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

Shinygeo ⭐ 35

Gene Expression Omnibus Analysis with Shiny 🔬

Rnaseq_titration_results ⭐ 29

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Volcano3d ⭐ 28

An R package to plot interactive three-way differential expression analysis

ASAP : Automated Single-cell Analysis Pipeline

Chromoformer ⭐ 24

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

GEDFN: Graph-Embedded Deep Feedforward Network

Rnaseq Pipeline ⭐ 18

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Neuroexpresso ⭐ 16

📊 Gene expression in neuroexpresso database

Pipernaseq ⭐ 16

A comprehensive pipeline for RNAseq data analysis

Gene-level general linear mixed model

Gene-level general linear mixed model

Tissuumapscore ⭐ 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.

Circompara ⭐ 12

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

Scinsight ⭐ 11

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data

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.

Adversarial Gene Expression ⭐ 8

Adversarial generation of gene expression data using Generative Adversarial Networks

Flexgsea R ⭐ 7

Flexible gene set enrichment analysis

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

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

KnowSeq R package

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.

Identification of candidate causal perturbations from differential gene expression data

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