Alternatives and similar repositories for piPipes

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

• smithlabcode / methpipe
  A pipeline for analyzing DNA methylation data from bisulfite sequencing.
  ☆70Updated 2 years ago
• zhqingit / giremi
  GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
  ☆44Updated 8 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆58Updated 2 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆89Updated 10 months ago
• khuang28jhu / bs3
  BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.
  ☆27Updated 6 years ago
• vastgroup / vast-tools
  A toolset for profiling alternative splicing events in RNA-Seq data.
  ☆81Updated 5 months ago
• guoweilong / cgmaptools
  toolbox for analysing BS-seq data, advance features in SNV, ASM and DMR
  ☆62Updated last year
• parklab / ShatterSeek
  ☆69Updated 2 years ago
• NYU-BFX / hic-bench
  A set of pipelines for Hi-C and ChIP-Seq analysis.
  ☆46Updated last year
• mhammell-laboratory / TElocal
  A package for quantifying transposable elements at a locus level for RNAseq datasets.
  ☆28Updated 5 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• ENCODE-DCC / dna-me-pipeline
  DCC/DAC methylation pipeline source
  ☆56Updated 4 years ago
• marvin-jens / find_circ
  tools to find circRNAs in RNA-seq data
  ☆43Updated 7 years ago
• BSSeeker / BSseeker2
  A versatile aligning pipeline for bisulfite sequencing data
  ☆65Updated 6 years ago
• BioinfoUNIBA / REDItools2
  ☆58Updated 3 years ago
• olarerin / metaPlotR
  A Perl/R pipeline for plotting metagenes
  ☆37Updated 3 years ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆109Updated 4 years ago
• LiuLabUB / HMMRATAC
  HMMRATAC peak caller for ATAC-seq data
  ☆100Updated 8 months ago
• IARCbioinfo / BAM-tricks
  Tip and tricks for BAM files
  ☆85Updated 6 years ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 6 years ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆114Updated 3 years ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆53Updated 4 years ago
• smithlabcode / dnmtools
  Tools for analyzing DNA methylation data
  ☆42Updated last week
• hms-dbmi / spp
  SPP - R package for analysis of ChIP-seq and other functional sequencing data
  ☆42Updated 4 years ago
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆74Updated 2 years ago
• tao-bioinfo / gff3sort
  GFF3sort: A Perl Script to sort gff3 files and produce suitable results for tabix tools
  ☆51Updated 5 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆97Updated 4 years ago
• cancerit / ascatNgs
  Somatic copy number analysis using WGS paired end wholegenome sequencing
  ☆72Updated 4 years ago
• patidarr / ngs_pipeline
  Exome/Capture/RNASeq Pipeline Implementation using snakemake
  ☆47Updated 7 years ago