91 Open source projects that are alternatives of or similar to anndata2ri

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

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

R package to do the Ligand Receptor Analysis Visualization

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/

Bioconductor package for management of multi-assay data

Single-cell copy number calling and event history reconstruction.

Dynamical systems methods for RNA velocity analysis

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

Manuscript for functional prediction of transcriptomic “dark matter” across species

Simulating single-cell data using gene regulatory networks 📠

Conversion between scRNA-seq objects

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

Modeling and correcting fragment sequence bias for RNA-seq

📚 R interface to the Bio-Formats library

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

MaAsLin2: Microbiome Multivariate Association with Linear Models

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

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

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Papers with code for single cell related papers

Next-Gen Sequencing tools from the Horvath Lab

Quantitative features for mass spectrometry data

Conditional out-of-distribution prediction

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

A R framework for pipeline benchmarking, with application to single-cell RNAseq

tidy processing of biological sequences in R

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

Import and summarize transcript-level estimates for gene-level analysis

A tool that allows to get UMI counts from a single cell protein assay

Contribute Packages to Bioconductor

Software for exploration of gene expression data from single-cell RNA sequencing.

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Mouse cell atlas

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

Clone identification from single-cell data

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

This is the ensembldb development repository.

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

This python package is for transitioning bioconductor from SVN to git

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

R package to visualize gene expression data based on weighted kernel density estimation

Reference mapping for single-cell genomics

Provide R access to the NCI Genomic Data Commons portal.

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

Computable build reports, package metadata, and download stats from the Bioconductor project

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.

Single cell analysis in the browser

Materials on the analysis of microarray expression data; focus on re-analysis of public data ( http://tinyurl.com/cruk-microarray)

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

Interactive R package to quantify, analyse and visualise alternative splicing