86 Open source projects that are alternatives of or similar to scTCRseq

Deep Learning based cell composition analysis with Scaden.

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

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

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

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

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

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

FEELnc : FlExible Extraction of LncRNA

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

Next-Gen Sequencing tools from the Horvath Lab

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

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

Multi-omics analysis protocols by Lyu.

Feature extraction algorithm for genomic data

Fast and accurate gene fusion detection from RNA-Seq data

Streamlining SLAM-seq analysis with ultra-high sensitivity

A versatile sequenced read processor for nanopore direct RNA sequencing

Porting DESeq2 and DEXSeq into python via rpy2

A collection of 50+ trajectory inference methods within a common interface 📥📤

CellRank for directed single-cell fate mapping

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

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

A pipeline for the computational evaluation of RNA-Seq data

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

CellNet: network biology applied to stem cell engineering

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

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

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

Version 2.1.0 released

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

🐍 Snakefiles for common RNA-seq data analysis workflows.

RNASeq pipeline

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

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

A proof of concept RNA-Seq pipeline with Nextflow

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

All-in-one analysis pipeline

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

Scripts to import your FeatureCounts output into DEXSeq

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

Fast in-silico normalization algorithm for NGS data

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

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.

RNA-seq analysis pipeline for detection gene-fusions

Wasserstein Generative Adversarial Network for analysing scRNAseq data

Summer school course materials collection

Single cell analysis in the browser

Reference-based transcript discovery from long RNA read

A Bayesian model for compositional single-cell data analysis

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

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

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

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

An automated RNA-seq pipeline using Nextflow

CWL tools and workflows for GGR

Spatial Single Cell Analysis in Python

Differential Gene Correlation Analysis

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

📊 Graphical User Interface for TCC package

Dynamical systems methods for RNA velocity analysis