Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing
☆18Updated this week
Alternatives and similar repositories for SCOTCH
Users that are interested in SCOTCH are comparing it to the libraries listed below
Sorting:
- Integrating long read sequencing enhances short read-based locus-specific transposable element quantification☆10May 12, 2025Updated 9 months ago
- Codes for the Iso-Seq variant-calling paper☆11Apr 28, 2023Updated 2 years ago
- FLAME: Full Length Adjecency Matrix Enumeration - is a module that allows for the analysis of ONT Nanopore RNA long-read sequencing data.…☆12May 8, 2025Updated 9 months ago
- The Flexible Demultiplexer☆40Updated this week
- 10X single cell Nanopore reads simulation workflow. Complete documentation avialable at: https://GenomiqueENS.github.io/AsaruSim/☆13Jul 27, 2025Updated 7 months ago
- ☆64Sep 19, 2025Updated 5 months ago
- LongSom tool for long-reads☆11May 20, 2025Updated 9 months ago
- Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.☆31Nov 6, 2025Updated 3 months ago
- single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single m…☆26Jul 20, 2024Updated last year
- ☆20Oct 5, 2022Updated 3 years ago
- ☆105Jan 23, 2026Updated last month
- A Cloud Pipeline to Analyze Long Read Sequencing Data from Oxford Nanopore and PacBio Sequencers☆12Jan 30, 2023Updated 3 years ago
- ☆31Nov 28, 2024Updated last year
- Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data☆12Dec 11, 2025Updated 2 months ago
- DOLPHIN: Advances Single-cell RNA-seq Analysis Beyond Gene-Level by Integrating Exon-Level Quantification and Junction Reads with Deep Ne…☆14Jul 16, 2025Updated 7 months ago
- Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome☆72Jan 31, 2024Updated 2 years ago
- Single cell Nanopore sequencing data for Genotype and Phenotype☆57May 15, 2025Updated 9 months ago
- ScisorWiz: Differential Isoform Visualizer for Long-Read RNA Sequencing Data☆20Apr 24, 2024Updated last year
- Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu☆15Feb 20, 2026Updated last week
- Iso-Seq reads simulator for PacBio and ONT full-length isoform sequencing technologies☆16Mar 1, 2022Updated 4 years ago
- A pipeline to detect chimeric transcripts derived from genes and transposable elements.☆35Jul 27, 2025Updated 7 months ago
- Long read to rMATS☆32May 5, 2023Updated 2 years ago
- Nanopore Real-Time Analysis Tool☆17Sep 4, 2024Updated last year
- R package to detect splicing QTLs (sQTLs)☆13Jul 3, 2023Updated 2 years ago
- Tools for detecting alternative splicing events and genotype in single-cell gene expression data.☆15Jan 16, 2024Updated 2 years ago
- The Isoforms from Single-Cell; Long-read Expression Suite☆38Jan 14, 2025Updated last year
- Long-read splice alignment with high accuracy☆64Sep 26, 2024Updated last year
- Invertory of TE-gene isoforms☆14Sep 18, 2023Updated 2 years ago
- Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files☆15Apr 4, 2024Updated last year
- Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.☆16May 17, 2022Updated 3 years ago
- Transcript assembly and quantification for RNA-Seq☆12Jun 3, 2019Updated 6 years ago
- This repository contains the code for reproducing all the results and figures from the preprint "Isoform specificity in the mouse primary…☆16Jul 16, 2021Updated 4 years ago
- ☆19Jan 24, 2025Updated last year
- Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis☆35Dec 17, 2021Updated 4 years ago
- LongcallR is a SNP caller for single molecule long-read RNA-seq data☆72Dec 14, 2025Updated 2 months ago
- Detection of m6A from direct RNA-Seq data☆131May 19, 2025Updated 9 months ago
- scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two cond…☆43Mar 9, 2023Updated 2 years ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆252Updated this week
- ☆20May 24, 2025Updated 9 months ago