134 Open source projects that are alternatives of or similar to ORNA

GREIN : GEO RNA-seq Experiments Interactive Navigator

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

The MG-RAST Backend -- the API server

🐍 Snakefiles for common RNA-seq data analysis workflows.

A pipeline for the computational evaluation of RNA-Seq data

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

RNASeq pipeline

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

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

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

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

CellNet: network biology applied to stem cell engineering

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

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

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

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

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

FEELnc : FlExible Extraction of LncRNA

Dynamical systems methods for RNA velocity analysis

Differential Gene Correlation Analysis

Porting DESeq2 and DEXSeq into python via rpy2

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

Fast and accurate gene fusion detection from RNA-Seq data

Summer school course materials collection

Version 2.1.0 released

Reference-based transcript discovery from long RNA read

MaAsLin2: Microbiome Multivariate Association with Linear Models

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

Feature extraction algorithm for genomic data

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

Class Normalization for Continual Zero-Shot Learning

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

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

CWL tools and workflows for GGR

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

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

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Next-Gen Sequencing tools from the Horvath Lab

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

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

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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

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

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

A proof of concept RNA-Seq pipeline with Nextflow

Text Normalization & Inverse Text Normalization

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

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

Scripts to import your FeatureCounts output into DEXSeq

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

Single cell analysis in the browser

RNA-seq analysis pipeline for detection gene-fusions

Collection of custom layers and utility functions for Keras which are missing in the main framework.

This package has migrated to https://github.com/rezakj/iCellR please use iCellR instead of scSeqR for more functionalities and updates.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

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