48 Open source projects that are alternatives of or similar to vidger

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

Interactive R package to quantify, analyse and visualise alternative splicing

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

Data-driven Network-based Bayesian Inference of Drivers

The Read Origin Protocol (ROP) is a computational protocol that aims to discover the source of all reads, including those originating from repeat sequences, recombinant B and T cell receptors, and microbial communities.

Porting DESeq2 and DEXSeq into python via rpy2

Discrete Distributional Differential Expression

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

interactive Multi Objective K-mer Analysis

Fit generalized linear models in python.

📊 Gene expression in neuroexpresso database

Tutorials, workflows, and convenience scripts for Single Cell Portal

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

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

Simplify your ETL processes with these hands-on data sanitation tips, tricks, and best practices

Interactive visualizations for differential expression

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Differential expression analysis for single-cell RNA-seq data.

Transcripts annotation and GO enrichment Fisher tests

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

Differential Gene Correlation Analysis

TCGA data acquisition and processing for Project Cognoma

Scalable RNA-seq analysis

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Spatial alignment of single cell transcriptomic data.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

R package to access DoRothEA's regulons

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Snakemake based pipeline for RNA-Seq analysis

Workshop on tidytranscriptomics: Performing tidy transcriptomics analyses with tidybulk, tidyverse and tidyheatmap

Fast in-silico normalization algorithm for NGS data

command line bioinformatic scripts written in R

Fast visualization tool for large-scale and high dimensional single-cell data

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

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

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

Reference mapping for single-cell genomics

Experimental design framework for scRNAseq population studies (eQTL and DE)

Compare different differential abundance and expression methods

A set of tools for working with JSON, CSV and Excel workbooks