Alternatives and similar repositories for squid:

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

• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆34Updated 7 years 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
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 3 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated last week
• jmw86069 / splicejam
  Sashimi plots for RNA-seq data using detected transcripts
  ☆27Updated 2 months ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• shawnzhangyx / PePr
  a peak-calling and differential analysis tool for replicated ChIP-Seq data
  ☆37Updated 2 years ago
• bartongroup / RATS
  Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.
  ☆32Updated 2 years ago
• lamortenera / epicseg
  Chromatin segmentation in R
  ☆19Updated 7 years ago
• Danko-Lab / tutorials
  Tutorials covering various topics in genomic data analysis.
  ☆16Updated 6 years ago
• olgabot / sj2psi
  Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores
  ☆8Updated 9 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆28Updated 7 months ago
• cfce / chilin
  ChIP-seq DC and QC Pipeline
  ☆34Updated 3 years ago
• churchill-lab / emase
  Expectation-Maximization algorithm for Allele-Specific Expression
  ☆21Updated last year
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆30Updated 6 years ago
• imbforge / NGSpipe2go
  a set of NGS pipelines
  ☆24Updated this week
• ExpressionAnalysis / HLAProfiler
  Using k-mers to call HLA alleles in RNA sequencing data
  ☆22Updated 6 years ago
• mskcc / lohhla
  Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
  ☆30Updated last year
• ChristopherWilks / snaptron
  fast webservices based query tool for large sets of genomic features
  ☆25Updated 2 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated last month
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆42Updated 3 years ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• Clinical-Genomics / fusion-report
  Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.githu…
  ☆26Updated 3 months ago
• d3b-center / annoFuse
  Filter and prioritize fusion calls
  ☆20Updated 5 months ago
• eyzhao / hrdetect-pipeline
  ☆34Updated 5 years ago
• pughlab / bamgineer
  Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets
  ☆37Updated 4 years ago