74 Open source projects that are alternatives of or similar to squid

Fast and accurate gene fusion detection from RNA-Seq data

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

RNA-seq analysis pipeline for detection gene-fusions

Single cell analysis in the browser

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

Deep Learning based cell composition analysis with Scaden.

GREIN : GEO RNA-seq Experiments Interactive Navigator

Fast in-silico normalization algorithm for NGS data

RNASeq pipeline

A method for circular DNA detection based on probabilistic mapping of ultrashort reads

CWL tools and workflows for GGR

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

Tools for processing and analyzing structural variants.

📊 Graphical User Interface for TCC package

The Modular Aligner and The Modular SV Caller

simuG: a general-purpose genome simulator

Reference-based transcript discovery from long RNA read

CellNet: network biology applied to stem cell engineering

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

🐍 Snakefiles for common RNA-seq data analysis workflows.

Dynamical systems methods for RNA velocity analysis

Pipeline for annotating genomes using long read transcriptomics data with pinfish

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

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

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

Structural Variation and fusion detection using targeted sequencing data from circulating cell free DNA

A pipeline for the computational evaluation of RNA-Seq data

Differential Gene Correlation Analysis

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

Scripts to import your FeatureCounts output into DEXSeq

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

Population-wide Deletion Calling

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

An automated RNA-seq pipeline using Nextflow

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

Multi-omics analysis protocols by Lyu.

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

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

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)

Next-Gen Sequencing tools from the Horvath Lab

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

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

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.

Identification of segmental duplications in the genome

Version 2.1.0 released

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

Feature extraction algorithm for genomic data

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

A proof of concept RNA-Seq pipeline with Nextflow

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

Summer school course materials collection

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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

Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data