Alternatives and similar repositories for KNIFE:

Users that are interested in KNIFE are comparing it to the libraries listed below

• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆42Updated 7 years ago
• orzechoj / circRNA_finder
  Pipeline for finding circular RNAs from RNA-seq data, based on STAR. Used in (Westholm et al, Cell Reports, 2014).
  ☆16Updated 2 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…
  ☆35Updated last year
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 6 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆41Updated 9 years ago
• heathsc / gemBS
  gemBS is a bioinformatics pipeline designed for high throughput analysis of DNA methylation from Whole Genome Bisulfite Sequencing data (…
  ☆33Updated 3 years ago
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆60Updated 5 years ago
• brwnj / fastq-multx
  Demultiplexes a fastq.
  ☆44Updated 4 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆38Updated 3 years ago
• pinellolab / AmpUMI
  Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)
  ☆41Updated 9 months ago
• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆29Updated 6 years ago
• ratschlab / RiboDiff
  RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data
  ☆23Updated 8 years ago
• saketkc / rna-seq-snakemake
  Snakemake based pipeline for RNA-Seq analysis
  ☆31Updated 5 years ago
• namphuon / ViFi
  Pipeline for identifying viral integration and fusion mRNA reads from NGS data. Manuscript is currently in preparation.
  ☆27Updated 3 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆39Updated 2 years ago
• dieterich-lab / DCC
  DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies …
  ☆36Updated 2 years ago
• WGLab / LIQA
  Long-read Isoform Quantification and Analysis
  ☆39Updated last month
• BioinfoUNIBA / QEdit
  RNA editing quantification in deep transcriptome data
  ☆15Updated 2 years ago
• Danko-Lab / tutorials
  Tutorials covering various topics in genomic data analysis.
  ☆16Updated 6 years ago
• bgruening / galaxy-rna-workbench
  Galaxy RNA workbench
  ☆39Updated 4 years ago
• YangLab / CLEAR
  direct comparison of circular and linear RNA expression
  ☆21Updated 4 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• dnaase / Bis-tools
  A collection of tools to deal with Bisulfite-seq/NOMe-seq (SNP/Methylation calling: BisSNP; HMM segmentation: DMNTools; Visualization/Clu…
  ☆31Updated 3 years ago
• rajewsky-lab / find_circ2
  Find circRNAs in RNA-seq data.
  ☆14Updated 8 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆36Updated 3 weeks ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• Bioconductor / copy-number-analysis
  Explore, compare, and evaluate Bioconductor packages related to genomic copy number analysis
  ☆21Updated last year
• zd1 / telseq
  A software for calculating telomere length
  ☆68Updated 6 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year