Alternatives and similar repositories for cloneHD:

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

• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• jmw86069 / splicejam
  Sashimi plots for RNA-seq data using detected transcripts
  ☆28Updated 3 weeks ago
• pachterlab / aggregationDE
  Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter
  ☆19Updated 7 years ago
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆35Updated 7 years ago
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆32Updated 2 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 3 years ago
• ChristopherWilks / snaptron
  fast webservices based query tool for large sets of genomic features
  ☆25Updated 2 weeks ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 2 months ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 7 years ago
• COMBINE-lab / SalmonTools
  Useful tools for working with Salmon output
  ☆37Updated 4 years ago
• ratschlab / mmr
  A tool for Read Multi-Mapper Resolution
  ☆23Updated 8 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• bcbio / bcbio_validations
  Validation runs using bcbio: germline, somatic, structural variant calling and RNA-seq analyses
  ☆31Updated 3 years ago
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• gagneurlab / OUTRIDER
  OUTRIDER: OUTlier in RNA-seq fInDER is an R-based framework to find aberrantly expressed genes in RNA-seq data
  ☆50Updated this week
• guigolab / grape-nf
  An automated RNA-seq pipeline using Nextflow
  ☆37Updated 6 months ago
• kauralasoo / wiggleplotr
  A small R package to make sequencing read coverage plots in R.
  ☆37Updated 2 years ago
• kgori / sigfit
  Flexible Bayesian inference of mutational signatures
  ☆34Updated 2 years ago
• churchill-lab / emase
  Expectation-Maximization algorithm for Allele-Specific Expression
  ☆21Updated last year
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 8 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆21Updated last year
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 8 years ago
• Danko-Lab / rtfbs_db
  Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
  ☆22Updated 6 years ago
• lamortenera / epicseg
  Chromatin segmentation in R
  ☆19Updated 7 years 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.
  ☆48Updated 5 years ago