Miscellaneous collection of Python and R scripts for processing Iso-Seq data
☆282Sep 26, 2023Updated 2 years ago
Alternatives and similar repositories for cDNA_Cupcake
Users that are interested in cDNA_Cupcake are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads☆241Jun 24, 2026Updated last month
- Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)☆185Apr 12, 2023Updated 3 years ago
- Tool for the Quality Control of Long-Read Defined Transcriptomes☆275Updated this week
- SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3☆38Jun 14, 2020Updated 6 years ago
- Technology agnostic long read analysis pipeline for transcriptomes☆160Jan 25, 2024Updated 2 years ago
- 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.
- Coding Genome Reconstruction using Iso-Seq data☆60Oct 20, 2021Updated 4 years ago
- CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)☆127Mar 18, 2024Updated 2 years ago
- ☆14Mar 13, 2018Updated 8 years ago
- Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.☆24Sep 24, 2015Updated 10 years ago
- classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF☆276Jul 7, 2026Updated 2 weeks ago
- PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.☆295Feb 4, 2025Updated last year
- Version II of Mandalorion☆32Feb 1, 2019Updated 7 years ago
- Full-Length Alternative Isoform analysis of RNA☆254Jun 23, 2026Updated last month
- Correct mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome☆72Jan 31, 2024Updated 2 years 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.
- Long read to rMATS☆32May 5, 2023Updated 3 years ago
- Error correction of ONT transcript reads☆58Sep 6, 2023Updated 2 years ago
- Fast and accurately polish the genome generated by long reads.☆243Jan 9, 2025Updated last year
- Long Reads Annotation pipeline☆71Mar 31, 2022Updated 4 years ago
- Transcript assembly and quantification for RNA-Seq☆525Jun 3, 2026Updated last month
- single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single m…☆27Mar 3, 2026Updated 4 months ago
- single-cell analysis workflows for double phosphoramidite barcode and UMI Correction (scCOLOR-seq)☆13Jul 13, 2023Updated 3 years ago
- Full-length transcriptome splicing and mutation analysis☆93Mar 23, 2026Updated 4 months ago
- A pipeline for isoseq☆23Jun 8, 2018Updated 8 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also…☆217Jun 30, 2026Updated 3 weeks ago
- PASA software☆202Feb 12, 2025Updated last year
- ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data☆179Oct 20, 2024Updated last year
- A universal toolkit for upstream processing of long RNA reads☆233Updated this week
- haplotypic duplication identification tool☆291Oct 30, 2025Updated 8 months ago
- Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…☆80Mar 21, 2023Updated 3 years ago
- k-mer based assembly evaluation☆351Jul 6, 2026Updated 2 weeks ago
- Create a pseudohaploid assembly from a partially resolved diploid assembly☆32Nov 22, 2019Updated 6 years ago
- Fast and accurate de novo assembler for long reads☆405May 10, 2024Updated 2 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- ☆39Apr 25, 2023Updated 3 years ago
- A versatile pairwise aligner for genomic and spliced nucleotide sequences☆2,220May 19, 2026Updated 2 months ago
- Long-reads Gap-free Chromosome-scale Assembler☆79Mar 21, 2023Updated 3 years ago
- SUPPA: Fast quantification of splicing and differential splicing☆306Nov 6, 2025Updated 8 months ago
- Long-read Isoform Quantification and Analysis☆40Mar 25, 2025Updated last year
- Tools for fast and flexible genome assembly scaffolding and improvement☆571Feb 14, 2024Updated 2 years ago
- Long read based human genomic structural variation detection with cuteSV☆291Jul 12, 2026Updated last week