Alternatives and similar repositories for KNIFE

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

• Jeltje / varscan2
  Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2
  ☆30Updated 7 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 …
  ☆37Updated 3 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…
  ☆36Updated 2 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 7 years ago
• AndreasHeger / gat
  Genomic Association Tester
  ☆34Updated 2 years ago
• hbctraining / Intro-to-rnaseq-hpc-salmon
  ☆50Updated 4 years ago
• bcgsc / HLAminer
  ⛏ HLA predictions from NGS shotgun data
  ☆55Updated 5 months ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• EI-CoreBioinformatics / portcullis
  Splice junction analysis and filtering from BAM files
  ☆42Updated 3 years ago
• dariober / bioinformatics-cafe
  Unsorted scripts for bioinformatics
  ☆61Updated 4 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆43Updated 4 years ago
• YangLab / CIRCexplorer
  A combined strategy to identify circular RNAs (circRNAs and ciRNAs) (Zhang et al., Complementary Sequence-Mediated Exon Circularization, …
  ☆62Updated 6 years ago
• s-andrews / BamQC
  Mapped QC analysis program
  ☆44Updated 7 years ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆41Updated 3 years ago
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆34Updated 3 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆37Updated 4 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆44Updated 8 years ago
• wyguo / ThreeDRNAseq
  A pipeline for differential expression and differential alternative splicing analysis
  ☆66Updated last year
• chrisamiller / readDepth
  R package for inferring copy number from read depth
  ☆32Updated 3 years ago
• brwnj / fastq-multx
  Demultiplexes a fastq.
  ☆48Updated 4 years ago
• snystrom / memes
  An R interface to the MEME Suite
  ☆53Updated 5 months ago
• zd1 / telseq
  A software for calculating telomere length
  ☆72Updated 7 years ago
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆99Updated last year
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆44Updated this week
• jsh58 / DMRfinder
  Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data
  ☆28Updated 2 years ago
• a-slide / NanoCount
  EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
  ☆64Updated last year
• lfresard / blood_rnaseq_rare_disease_paper
  ☆29Updated 6 years ago
• imbforge / NGSpipe2go
  a set of NGS pipelines
  ☆24Updated last month
• nf-core / lncpipe
  UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
  ☆34Updated 7 months ago