70 Open source projects that are alternatives of or similar to diffexpr

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

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

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

An automated RNA-seq pipeline using Nextflow

Fast and accurate gene fusion detection from RNA-Seq data

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

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

Interactive visualizations for differential expression

command line bioinformatic scripts written in R

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

A graphical user interface for distributed data processing of high throughput genomics

CWL tools and workflows for GGR

Scripts to import your FeatureCounts output into DEXSeq

A pipeline for the computational evaluation of RNA-Seq data

Multi-omics analysis protocols by Lyu.

Lightweight and Fast; RNA-seq quantification at the event-level

A versatile sequenced read processor for nanopore direct RNA sequencing

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

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

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

🐍 Snakefiles for common RNA-seq data analysis workflows.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Version 2.1.0 released

A proof of concept RNA-Seq pipeline with Nextflow

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Processing of single cell RNAseq data for the recovery of TCRs in python

Feature extraction algorithm for genomic data

Reference-based transcript discovery from long RNA read

A tool to identify, orient, trim and rescue full length cDNA reads

Single cell analysis in the browser

RNA-seq analysis pipeline for detection gene-fusions

📊 Graphical User Interface for TCC package

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Deep Learning based cell composition analysis with Scaden.

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

Fast in-silico normalization algorithm for NGS data

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

Next-Gen Sequencing tools from the Horvath Lab

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

CellNet: network biology applied to stem cell engineering

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

RNASeq pipeline

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

Dynamical systems methods for RNA velocity analysis

Summer school course materials collection

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

Fit generalized linear models in python.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

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.

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

Discrete Distributional Differential Expression

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

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly