Other Open Access

DNase-seq and histone mark ChIP-seq convolutional autoencoders

Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter


JSON-LD (schema.org) Export

{
  "description": "<p>We provide 6 convolutional autoencoders for encoding DNase-seq and histone mark ChIP-seq regions of 3 kilobase pairs, 12 kilobase pairs, and 120 kilobase pairs at 25 base pair, 100 base pair, and 1000 base pair resolution respectively. The histone mark ChIP-seq autoencoders were trained on 49 experiments from the <a href=\"http://www.roadmapepigenomics.org\">Roadmap Epigenetics</a> projects targeting&nbsp;H3K4me1, H3K4me3, H3K27ac, H3K9ac, H3K27me3, H3K9me3, and H3K36me (see experiment IDs below). The DNase-seq autoencoders were trained on 120 experiments from the <a href=\"https://www.encodeproject.org\">ENCODE projects</a>&nbsp;(see accession numbers below).</p>\n\n<p>These autoencoders were produced as part of the <a href=\"http://peax.lekschas.de\">Peax project</a>.</p>\n\n<p>Roadmap Epigenomics experiment IDs:</p>\n\n<p>E003, E004, E005, E006, E007, E008, E011, E014, E015, E016, E017, E019, E020, E026, E038, E047, E049, E062, E063, E066, E067, E068, E069, E072, E073, E074, E075, E076, E087, E101, E102, E103, E108, E111, E114, E115, E116, E117, E118, E119, E120, E121, E122, E123, E124, E125, E126, E127, E128</p>\n\n<p>ENCODE access numbers:</p>\n\n<p>ENCSR000EQB (2), ENCSR316UDN (1), ENCSR317SIH (1), ENCSR000EJO (1), ENCSR038XTK (1), ENCSR158VAT (1), ENCSR680SDS (1), ENCSR440FZS (1), ENCSR678PDD (1), ENCSR299INS (1), ENCSR000ENZ (1), ENCSR121ZSL (1), ENCSR796SJV (1), ENCSR035QHH (1), ENCSR515EWI (2), ENCSR000EQD (1), ENCSR271QSV (1), ENCSR426IEA (1), ENCSR000EPG (2), ENCSR000EIY (1), ENCSR595CSH (1), ENCSR000EQJ (1), ENCSR383BLX (1), ENCSR628IRM (1), ENCSR477RTP (1), ENCSR512CWR (1), ENCSR000EQI (1), ENCSR945RWN (1), ENCSR272RQX (1), ENCSR814KRX (1), ENCSR548MMD (1), ENCSR141VGA (1), ENCSR645GJD (1), ENCSR594NOE (1), ENCSR691MQJ (2), ENCSR000EPI (1), ENCSR381PXW (1), ENCSR468ZXN (1), ENCSR000EPE (2), ENCSR434OBM (1), ENCSR931UQB (1), ENCSR217RVH (1), ENCSR325LYJ (1), ENCSR004SUL (1), ENCSR035RVH (1), ENCSR217TAW (1), ENCSR184LMY (1), ENCSR940NLN (1), ENCSR000FFJ (1), ENCSR153LHP (1), ENCSR383SNM (1), ENCSR052AWE (1), ENCSR672EWY (2), ENCSR098PTC (2), ENCSR452DCM (1), ENCSR265TEK (1), ENCSR852TRT (1), ENCSR120LVW (1), ENCSR251UPG (1), ENCSR564JUY (1), ENCSR782XFY (1), ENCSR774RCO (1), ENCSR405TXU (1), ENCSR154ZNQ (1), ENCSR257BGZ (1), ENCSR148VUP (1), ENCSR593LTJ (1), ENCSR622TWS (1), ENCSR649KBB (1), ENCSR000ELO (1), ENCSR696TPW (1), ENCSR191EII (1), ENCSR019JDO (1), ENCSR000EML (1), ENCSR458LIB (2), ENCSR269SIA (2), ENCSR000EMR (1), ENCSR385AMY (1), ENCSR208DMX (1), ENCSR033STL (1), ENCSR683QJJ (1), ENCSR845CFB (1), ENCSR228VNQ (2), ENCSR517NHP (1), ENCSR337IRF (1), ENCSR000EPK (2), ENCSR554WUJ (1), ENCSR770DEN (1), ENCSR724CND (1), ENCSR911LTI (1), ENCSR857AEB (1), ENCSR959ZXU (1), ENCSR000EPD (1), ENCSR714DIF (1), ENCSR141NSQ (1), ENCSR083STA (1), ENCSR346IHH (1), ENCSR164WOF (1), ENCSR224FOA (2), ENCSR000EJQ (1), ENCSR621ENC (1), ENCSR228IKB (1), ENCSR954AJK (1), ENCSR206FSY (1), ENCSR275ICP (1), ENCSR552XJI (1), ENCSR445XYW (1), ENCSR166KPV (1), ENCSR935EVZ (1), ENCSR236SFP (1), ENCSR792ZXA (1), ENCSR426TPQ (1), ENCSR582IPV (2), ENCSR524OCB (1), ENCSR000EMV (1), ENCSR902XFY (1), ENCSR000EIS (1), ENCSR921NMD (1), ENCSR873ANE (1), ENCSR850YHJ (1)</p>\n\n<p>In paratheses are the replicate IDs.</p>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Harvard University", 
      "@id": "https://orcid.org/0000-0001-8432-4835", 
      "@type": "Person", 
      "name": "Lekschas, Fritz"
    }, 
    {
      "affiliation": "Novartis Institutes for BioMedical Research", 
      "@type": "Person", 
      "name": "Peterson, Brant"
    }, 
    {
      "affiliation": "Harvard University", 
      "@id": "https://orcid.org/0000-0001-9144-3461", 
      "@type": "Person", 
      "name": "Haehn, Daniel"
    }, 
    {
      "affiliation": "Novartis Institutes for BioMedical Research", 
      "@id": "https://orcid.org/0000-0003-0041-5989", 
      "@type": "Person", 
      "name": "Ma, Eric"
    }, 
    {
      "affiliation": "Harvard Medical School", 
      "@id": "https://orcid.org/0000-0003-0327-8297", 
      "@type": "Person", 
      "name": "Gehlenborg, Nils"
    }, 
    {
      "affiliation": "Harvard University", 
      "@id": "https://orcid.org/0000-0002-3620-2582", 
      "@type": "Person", 
      "name": "Pfister, Hanspeter"
    }
  ], 
  "url": "https://zenodo.org/record/2609763", 
  "datePublished": "2019-03-26", 
  "version": "1.0.0", 
  "keywords": [
    "Autoencoder", 
    "CNN", 
    "DNase-seq", 
    "ChIP-seq", 
    "histone mark ChIP-seq"
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.2609763", 
  "@id": "https://doi.org/10.5281/zenodo.2609763", 
  "@type": "CreativeWork", 
  "name": "DNase-seq and histone mark ChIP-seq convolutional autoencoders"
}
177
45
views
downloads
All versions This version
Views 177177
Downloads 4545
Data volume 5.7 GB5.7 GB
Unique views 164164
Unique downloads 1414

Share

Cite as