Alternatives and similar repositories for juicer

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

• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆415Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆429Updated this week
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆448Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆478Updated last week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆426Updated 7 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆256Updated 2 years ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆458Updated 3 weeks ago
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆519Updated 4 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆515Updated last month
• snakemake-workflows / rna-seq-star-deseq2
  RNA-seq workflow using STAR and DESeq2
  ☆344Updated last year
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆375Updated 3 years ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆436Updated 2 years ago
• deeptools / HiCExplorer
  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
  ☆253Updated 3 weeks ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆508Updated 8 months ago
• aidenlab / Juicebox
  Visualization and analysis software for Hi-C data -
  ☆265Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆726Updated 2 weeks ago
• mdozmorov / HiC_tools
  A collection of tools for Hi-C data analysis
  ☆600Updated 2 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆278Updated last year
• maxplanck-ie / snakepipes
  Customizable workflows based on snakemake and python for the analysis of NGS data
  ☆398Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆296Updated 10 months ago
• ENCODE-DCC / atac-seq-pipeline
  ENCODE ATAC-seq pipeline
  ☆426Updated last year
• broadinstitute / gtex-pipeline
  GTEx & TOPMed data production and analysis pipelines
  ☆376Updated 2 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆831Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆369Updated last month
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆466Updated last week
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆493Updated 2 years ago
• WGLab / doc-ANNOVAR
  Documentation for the ANNOVAR software
  ☆243Updated last week