Oshlack / necklaceView external linksLinks
Combine reference and assembled transcriptomes for RNA-Seq analysis
☆23Feb 12, 2020Updated 6 years ago
Alternatives and similar repositories for necklace
Users that are interested in necklace are comparing it to the libraries listed below
Sorting:
- Just Annotate My Genome☆19Sep 17, 2024Updated last year
- Building SuperTranscripts: A linear representation of transcriptome data☆68Mar 22, 2021Updated 4 years ago
- de novo targeted gene assembly☆22Apr 16, 2021Updated 4 years ago
- Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter☆19Feb 20, 2018Updated 7 years ago
- Software for clustering de novo assembled transcripts and counting overlapping reads☆76Feb 11, 2022Updated 4 years ago
- (check out instaGRAAL for a faster, updated program!) This program is from Marie-Nelly et al., Nature Communications, 2014 (High-qualit…☆15Nov 22, 2022Updated 3 years ago
- Process SMRT sequencing kinetic summary to predict regional methylation on large genome☆12Dec 4, 2018Updated 7 years ago
- Mostly deprecated in favor of : https://github.com/hbc/bcbioRNASeq. Quality control, differential gene/transcript expression and pathway …☆24Dec 11, 2017Updated 8 years ago
- Assembly by Reduced Complexity (ARC)☆42Mar 29, 2016Updated 9 years ago
- ☆23Nov 9, 2025Updated 3 months ago
- SALSA: A tool to scaffold long read assemblies with Hi-C data☆188May 17, 2024Updated last year
- BANDITS: Bayesian ANalysis of DIfferenTial Splicing☆19Sep 29, 2025Updated 4 months ago
- Pre-mAsking Long reads for Mobile Element inseRtion☆10Feb 27, 2023Updated 2 years ago
- A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.☆98Apr 9, 2023Updated 2 years ago
- SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3☆38Jun 14, 2020Updated 5 years ago
- ☆42Sep 14, 2022Updated 3 years ago
- Improved multi-sample transcript abundance estimates using adaptive priors☆20Oct 29, 2018Updated 7 years ago
- Shell bootloader for data science.☆12Feb 8, 2026Updated last week
- Trinotate annotation report summaries in R☆13Feb 24, 2016Updated 9 years ago
- stageR package☆13Feb 28, 2023Updated 2 years ago
- Nanopanel2: a somatic variant caller for Nanopore panel sequencing data☆11Sep 21, 2021Updated 4 years ago
- Docker container for Illumina bcl2fastq☆11Aug 7, 2024Updated last year
- Scripts and documentations on the MCSC decontamination method☆10Jun 13, 2023Updated 2 years ago
- Modeling gene duplication, loss, and coalescence (through parsimony)☆10Jun 18, 2020Updated 5 years ago
- Multisample Variant Format ToolKit☆10Oct 12, 2021Updated 4 years ago
- CNEFinder: Finding Conserved Non-coding Elements in Genomes☆25Jul 21, 2021Updated 4 years ago
- Helper scripts for processing and visualization of phylogenetics datasets☆31Feb 19, 2024Updated last year
- GAPPadder is tool for closing gaps on draft genomes with short sequencing data☆28Jun 1, 2017Updated 8 years ago
- PgRC: Pseudogenome based Read Compressor☆14Nov 20, 2024Updated last year
- Faster manipulation of dendrogram objects in R.☆15May 22, 2015Updated 10 years ago
- DNAscan2 is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring v…☆14May 7, 2024Updated last year
- Program for estimating admixture proportions and doing principal component analysis of a single NGS sample☆11Aug 15, 2024Updated last year
- Reproducible GSEA Benchmarking☆14Oct 30, 2025Updated 3 months ago
- integrative pathway analysis with modern PCA methodology and gene selection☆11Jun 29, 2023Updated 2 years ago
- Altered TCR Ligand Affinities and Structures☆12Dec 1, 2023Updated 2 years ago
- ☆10Mar 4, 2025Updated 11 months ago
- Keep Me Around: Intron Retention Detection☆30Jan 30, 2019Updated 7 years ago
- A program for fast and accurate genome-guided transcripts reconstruction and quantification from RNA-seq (Supporting Pacbio single-end)☆24Apr 21, 2021Updated 4 years ago
- Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA☆14Feb 16, 2023Updated 2 years ago