Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu
☆23Jul 28, 2026Updated this week
Alternatives and similar repositories for bambu-pipe
Users that are interested in bambu-pipe are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The Flexible Demultiplexer☆44Mar 30, 2026Updated 3 months ago
- Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files☆15Apr 4, 2024Updated 2 years ago
- Reference-guided transcript discovery and quantification for long read RNA-Seq data☆251Updated this week
- ☆115Jan 23, 2026Updated 6 months ago
- An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedo…☆18Sep 1, 2025Updated 10 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- SingleCell Nanopore sequencing data analysis☆69May 30, 2025Updated last year
- Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics☆56Updated this week
- IsoVis enables fast and informative visualization of isoform structures and expression levels.☆16Jun 19, 2026Updated last month
- Improving gene isoform quantification with miniQuant☆43Jan 13, 2026Updated 6 months ago
- ☆31Nov 28, 2024Updated last year
- Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project☆161Jan 23, 2026Updated 6 months ago
- Tools for detecting alternative splicing events and genotype in single-cell gene expression data.☆15Jan 16, 2024Updated 2 years ago
- EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2☆68Oct 11, 2024Updated last year
- Direct RNA publication scripts☆11Sep 20, 2017Updated 8 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Isoform-level spatial transcriptomics analysis☆17May 3, 2026Updated 2 months ago
- ☆67Mar 19, 2026Updated 4 months 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
- Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.☆38Nov 8, 2023Updated 2 years ago
- single-nucleus nanopore reads processing pipeline☆16Aug 16, 2023Updated 2 years ago
- Detection of m6A from direct RNA-Seq data☆133May 19, 2025Updated last year
- R package for visualization and exploratory analysis of Oxford Nanopore direct RNA seq based polyA predictions☆13Jun 25, 2024Updated 2 years ago
- Telomere-to-Telomere diploid Indian Genome☆15Mar 5, 2026Updated 4 months ago
- A gene fusion caller for long-read transcriptome sequencing data.☆22Apr 29, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆18Jan 13, 2025Updated last year
- Benchmarking long-read RNA-seq analysis tools☆28Feb 17, 2025Updated last year
- Pipeline to analyze long-read mRNA isoforms and ORF products sequenced in breast cancer using PacBio Single-Molecule technology.☆16May 17, 2022Updated 4 years ago
- Quantification of isoform usage and alternative polyadenylation (APA) from single-cell RNA-seq using a Nextflow-based pipeline.☆36Nov 6, 2025Updated 8 months ago
- Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)☆166Mar 19, 2026Updated 4 months ago
- ☆25Jul 30, 2025Updated 11 months ago
- fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector☆27Mar 9, 2026Updated 4 months ago
- A bioinformatics tool for viewing and calculating base modification frequencies from BAM files☆46Updated this week
- Identification of differential RNA modifications from nanopore direct RNA sequencing☆167Jul 17, 2026Updated last week
- 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.
- Code for the paper "A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes"☆20Oct 29, 2019Updated 6 years ago
- Tool to flag foldback and chimeric artifacts in long-read sequence alignment files☆42Jul 1, 2026Updated 3 weeks ago
- A curated list of awesome nanopore analysis tools.☆323May 20, 2026Updated 2 months ago
- Visualise and analyse nanopore (ONT) raw signals☆130Jun 11, 2026Updated last month
- (m)6A (I)dentification Using (N)anopor(E) (S)equencing☆19Nov 25, 2020Updated 5 years ago
- A Python library to visualize and analyze long-read transcriptomes☆69Jan 19, 2026Updated 6 months ago
- Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing☆15Aug 27, 2025Updated 11 months ago