Alternatives and similar repositories for squid:

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

• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• pachterlab / kma
  Keep Me Around: Intron Retention Detection
  ☆29Updated 6 years ago
• lamortenera / epicseg
  Chromatin segmentation in R
  ☆19Updated 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
• 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
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆28Updated 7 months ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 3 years ago
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 3 years ago
• carjed / helmsman
  highly-efficient & lightweight mutation signature matrix aggregation
  ☆19Updated 3 years ago
• jmw86069 / splicejam
  Sashimi plots for RNA-seq data using detected transcripts
  ☆27Updated 3 months ago
• CGGOxford / Opossum
  Opossum is a tool to pre-process RNA-seq reads prior to variant calling.
  ☆28Updated 6 years ago
• yuchaojiang / CODEX2
  Full-spectrum copy number variation detection by high-throughput DNA sequencing
  ☆37Updated 3 years ago
• AstraZeneca-NGS / disambiguate
  Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem
  ☆30Updated 6 years ago
• olgabot / sj2psi
  Convert RNA-STAR aligner "SJ.out.tab" files to "Percent spliced-in" (Psi) scores
  ☆8Updated 9 years ago
• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 8 years ago
• pachterlab / sircel
  Identify cell barcodes from single-cell genomics sequencing experiments
  ☆43Updated 3 years ago
• thelovelab / rnaseqDTU
  RNA-seq workflow: differential transcript usage
  ☆21Updated last year
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆27Updated 2 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 2 weeks ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated last year
• Wedge-lab / dpclust
  Dirichlet Process based methods for subclonal reconstruction of tumours
  ☆29Updated 5 months ago
• yuifu / millefy
  Millefy: Genome browser-like visualization of single-cell RNA-seq dataset
  ☆28Updated 5 years ago
• mskcc / ngs-filters
  Filters for false-positive mutation calls in NGS
  ☆30Updated 5 years ago
• mritchielab / GlimmaV2
  interactive plots for differential expression analysis
  ☆32Updated 3 weeks ago
• viq854 / lichee
  Multi-sample cancer phylogeny reconstruction
  ☆34Updated 7 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 2 months ago
• 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
• Danko-Lab / rtfbs_db
  Parse TF motifs from public databases, read into R, and scan using 'rtfbs'.
  ☆22Updated 6 years ago
• thelovelab / tximeta
  Transcript quantification import with automatic metadata detection
  ☆67Updated last month