Alternatives and similar repositories for Haystack

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

• rajanil / msCentipede
  A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.
  ☆26Updated 9 years ago
• ChristopherWilks / snaptron
  fast webservices based query tool for large sets of genomic features
  ☆25Updated 6 months ago
• ibn-salem / sevenC
  7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
  ☆13Updated last month
• mikelove / alpine
  Modeling and correcting fragment sequence bias for RNA-seq
  ☆24Updated last year
• SnakeChunks / SnakeChunks
  Modular blocks to build Snakemake workflows for reproducible NGS analyses
  ☆22Updated 6 years ago
• nellore / rail
  Scalable RNA-seq analysis
  ☆73Updated 4 years ago
• lamortenera / epicseg
  Chromatin segmentation in R
  ☆19Updated 7 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• OmnesRes / onco_lnc
  ☆35Updated 9 years ago
• jpiper / pyDNase
  Python module for the easy handling and analysis of DNase-seq data
  ☆37Updated 6 years ago
• JEFworks / ubit2
  User-friendly Bioinformatics Tools
  ☆18Updated 4 years ago
• lgautier / fastq-and-furious
  Efficient handling of FASTQ files from Python
  ☆51Updated last week
• slowkow / picardmetrics
  Run Picard on BAM files and collate 90 metrics into one file.
  ☆40Updated 8 years ago
• ueser / FIDDLE
  Flexible Integration of Data with Deep LEarning
  ☆51Updated 2 years ago
• mahmoudibrahim / JAMM
  JAMM Peak Finder for Sequencing Datasets
  ☆29Updated 5 years ago
• pachterlab / sleuth_paper_analysis
  Code to reproduce analyses from the sleuth paper
  ☆16Updated 7 years ago
• Teichlab / GPfates
  ☆21Updated 8 years ago
• kimpenn / VERSE
  A versatile and efficient RNA-Seq read counting tool
  ☆16Updated 9 years ago
• simonvh / fluff
  Fluff is a Python package that contains several scripts to produce pretty, publication-quality figures for next-generation sequencing exp…
  ☆71Updated last year
• kundajelab / training_camp
  Genetics training camp
  ☆21Updated 5 years ago
• nellore / intropolis
  Exon-exon splice junctions across SRA
  ☆42Updated 4 years ago
• CollasLab / edd
  Enriched Domain Detector for ChIP-seq data
  ☆16Updated 3 years ago
• kundajelab / genomedisco
  Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
  ☆26Updated 7 years ago
• kundajelab / coda
  Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data
  ☆33Updated 8 years ago
• boutroslab / cld
  A software for the multispecies design of CRISPR/Cas9 libraries
  ☆36Updated 3 years ago
• pinellolab / haystack_bio
  Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
  ☆47Updated 3 years ago
• biocore-ntnu / epic
  (DEPRECATED) epic: diffuse domain ChIP-Seq caller based on SICER
  ☆31Updated 7 years ago
• cancerit / cgpBigWig
  BigWig manpulation tools using libBigWig and htslib
  ☆29Updated last year
• ewels / Labrador
  A web based tool to manage and automate the processing of publicly available datasets.
  ☆39Updated 4 years ago
• brwnj / umitools
  Tools to handle reads sequenced with unique molecular identifiers (UMIs).
  ☆30Updated 8 years ago