47 Open source projects that are alternatives of or similar to tximport

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

Modeling and correcting fragment sequence bias for RNA-seq

Bioconductor package for management of multi-assay data

Contribute Packages to Bioconductor

A proof of concept RNA-Seq pipeline with Nextflow

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Analysing Capture Seq Count Data

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

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

Convert between AnnData and SingleCellExperiment

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

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

📚 R interface to the Bio-Formats library

Project Manager for NGS data analysis

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

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

This is the ensembldb development repository.

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

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

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

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

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

MaAsLin2: Microbiome Multivariate Association with Linear Models

This python package is for transitioning bioconductor from SVN to git

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

Provide R access to the NCI Genomic Data Commons portal.

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

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

Interactive R package to quantify, analyse and visualise alternative splicing

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

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

Quantitative features for mass spectrometry data

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

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

Conversion between scRNA-seq objects

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

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

tidy processing of biological sequences in R

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

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

Regulatory networks with Direct Information in python

Compare different differential abundance and expression methods

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

A proof of concept of RNAseq pipeline

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

hbctraining.github.io/intro-to-r-with-dge/