jts / nanopore-rna-analysis

Related projects ⓘ

Alternatives and complementary repositories for nanopore-rna-analysis

• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 2 years ago
• nanoporetech / pipeline-pinfish-analysis
  Pipeline for annotating genomes using long read transcriptomics data with pinfish
  ☆27Updated 3 years ago
• stephenturner / adapters
  Adapters for trimming
  ☆30Updated 5 years ago
• chizksh / digenome-toolkit2
  Digenome-toolkit ver2.
  ☆15Updated 3 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 6 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆56Updated last month
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆31Updated 2 years ago
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆32Updated 2 years ago
• cortes-ciriano-lab / ReConPlot
  ☆21Updated 2 weeks ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 2 years ago
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆48Updated 3 years ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆38Updated 2 years ago
• ENCODE-DCC / wgbs-pipeline
  ENCODE whole-genome bisulfite sequencing (WGBS) pipeline
  ☆29Updated 2 years ago
• ENCODE-DCC / long-read-rna-pipeline
  ENCODE long read RNA-seq pipeline
  ☆44Updated last year
• rvolden / Mandalorion-Episode-II
  Version II of Mandalorion
  ☆32Updated 5 years ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆24Updated 9 years ago
• SdeBlank / NanoFG
  Third-generation fusion gene detection
  ☆13Updated last year
• nf-core / lncpipe
  UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
  ☆33Updated 6 months ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 7 years ago
• biocorecrg / MOP2
  Master of Pores 2
  ☆23Updated last year
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 4 years ago
• stephenfloor / extract-transcript-regions
  For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…
  ☆33Updated last year
• compbiolabucf / AS-Quant
  Quantitation and visualization of differential alternative splicing events
  ☆9Updated last year
• Magdoll / SQANTI2
  SQANTI2 is now replaced by SQANTI3. Please go to: https://github.com/ConesaLab/SQANTI3
  ☆38Updated 4 years ago
• Kingsford-Group / rnaseqtools
  toolkit to process gtf files
  ☆16Updated 2 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆41Updated 2 years ago
• drostlab / myTAI
  Evolutionary Transcriptomics with R
  ☆41Updated this week
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆39Updated 3 years ago