93 Open source projects that are alternatives of or similar to scaden

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

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

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

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Reference-based transcript discovery from long RNA read

Feature extraction algorithm for genomic data

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

CWL tools and workflows for GGR

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

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

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

Summer school course materials collection

Version 2.1.0 released

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

A Bayesian model for compositional single-cell data analysis

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

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

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

Fast in-silico normalization algorithm for NGS data

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

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Differential Gene Correlation Analysis

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

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

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

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

CellRank for directed single-cell fate mapping

A pipeline for the computational evaluation of RNA-Seq data

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

DICOM Image Segmentation with CNNs in Tensorflow

🐍 Snakefiles for common RNA-seq data analysis workflows.

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

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

CellNet: network biology applied to stem cell engineering

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

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

All-in-one analysis pipeline

GREIN : GEO RNA-seq Experiments Interactive Navigator

Streamlining SLAM-seq analysis with ultra-high sensitivity

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

RNASeq pipeline

FEELnc : FlExible Extraction of LncRNA

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

Scripts to import your FeatureCounts output into DEXSeq

Next-Gen Sequencing tools from the Horvath Lab

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

Porting DESeq2 and DEXSeq into python via rpy2

Fast and accurate gene fusion detection from RNA-Seq data

Dynamical systems methods for RNA velocity analysis

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

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

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

A versatile sequenced read processor for nanopore direct RNA sequencing

Wasserstein Generative Adversarial Network for analysing scRNAseq data

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