Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.
☆36Nov 6, 2025Updated 8 months ago
Alternatives and similar repositories for SCALPEL
Users that are interested in SCALPEL are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Bioinformatics pipeline for single-cell 3' UTR isoform quantification☆33Jan 29, 2026Updated 5 months ago
- Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:☆23Mar 30, 2024Updated 2 years ago
- ☆55Aug 1, 2024Updated last year
- The Isoforms from Single-Cell; Long-read Expression Suite☆40Jan 14, 2025Updated last year
- Integrating long read sequencing enhances short read-based locus-specific transposable element quantification☆12May 12, 2025Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- DOLPHIN: Advances Single-cell RNA-seq Analysis Beyond Gene-Level by Integrating Exon-Level Quantification and Junction Reads with Deep Ne…☆14Jul 16, 2025Updated last year
- APA Regression Net - Predict and Engineer Alternative Polyadenylation☆43Oct 1, 2021Updated 4 years ago
- polyApipe☆22Feb 10, 2025Updated last year
- Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.☆38Nov 8, 2023Updated 2 years ago
- ☆21Aug 26, 2024Updated last year
- ☆24Jun 7, 2024Updated 2 years ago
- SpliceWiz is an R package for exploring differential alternative splicing events in splice-aware alignment BAM files.☆24Dec 10, 2025Updated 7 months ago
- Isoform-level functional RNA-Seq analysis 🧬☆39Jul 7, 2026Updated 2 weeks ago
- single-cell clustering based on alternative splicing landscapes☆23Mar 20, 2024Updated 2 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Detection and couting alternative TSS in single cells☆17Apr 21, 2024Updated 2 years ago
- Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single…☆25Jun 20, 2026Updated last month
- ☆67Mar 19, 2026Updated 4 months ago
- ☆37Jun 26, 2026Updated 3 weeks ago
- Gencode UTR fix☆17Jan 11, 2023Updated 3 years ago
- AIDA phase 1 splicing QTL paper☆16Feb 17, 2026Updated 5 months ago
- ☆19May 25, 2026Updated last month
- Lightweight Python interfaces for reading, writing, and querying genomic regions (BED)☆15Jul 10, 2026Updated last week
- Model-based analysis of APA using 3' end-linked reads☆13Aug 14, 2021Updated 4 years ago
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- ☆27Oct 22, 2025Updated 8 months ago
- Open4Gene, A Hurdle Model-based Method for Peak-to-Gene Linkage Analysis☆17Mar 17, 2026Updated 4 months ago
- Splicing-aware time-course network enricher - exploratory analysis for transcriptomics and/or proteomics time series data☆11Dec 11, 2025Updated 7 months ago
- scGRO-seq analyses codes☆13Jan 9, 2024Updated 2 years ago
- A gene fusion caller for long-read transcriptome sequencing data.☆22Apr 29, 2024Updated 2 years ago
- Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu☆23Jul 10, 2026Updated last week
- ☆14Feb 17, 2022Updated 4 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 last year
- APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach…☆13Apr 5, 2026Updated 3 months ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Codes for the Iso-Seq variant-calling paper☆11Apr 28, 2023Updated 3 years ago
- Just the leafviz parts of Leafcutter☆16Apr 2, 2026Updated 3 months ago
- Tools for detecting alternative splicing events and genotype in single-cell gene expression data.☆15Jan 16, 2024Updated 2 years ago
- Bullseye analysis pipeline for DART-seq analysis☆16May 25, 2026Updated last month
- Comprehensive and scalable differential splicing analyses☆18Dec 19, 2025Updated 7 months ago
- ☆17Jul 19, 2024Updated 2 years ago
- ☆28Jul 4, 2026Updated 2 weeks ago