2609763
doi
10.5281/zenodo.2609763
oai:zenodo.org:2609763
Peterson, Brant
Novartis Institutes for BioMedical Research
Haehn, Daniel
Harvard University
Ma, Eric
Novartis Institutes for BioMedical Research
Gehlenborg, Nils
Harvard Medical School
Pfister, Hanspeter
Harvard University
DNase-seq and histone mark ChIP-seq convolutional autoencoders
Lekschas, Fritz
Harvard University
doi:10.1101/597518
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Autoencoder
CNN
DNase-seq
ChIP-seq
histone mark ChIP-seq
<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 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> (see accession numbers below).</p>
<p>These autoencoders were produced as part of the <a href="http://peax.lekschas.de">Peax project</a>.</p>
<p>Roadmap Epigenomics experiment IDs:</p>
<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>
<p>ENCODE access numbers:</p>
<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>
<p>In paratheses are the replicate IDs.</p>
Zenodo
2019-03-26
info:eu-repo/semantics/other
2609762
1.0.0
1554866904.34848
125690600
md5:18097c07e61141254115991bf6259743
https://zenodo.org/records/2609763/files/chip_w-12000_r-100.h5
125690600
md5:ad07e8759bb5aed585171cfc1994bf69
https://zenodo.org/records/2609763/files/chip_w-120000_r-1000.h5
125690600
md5:8dbf5a7f7d3064eb4891d217eab45552
https://zenodo.org/records/2609763/files/chip_w-3000_r-25.h5
125690600
md5:397ee368a676b97117bdd4c83290627f
https://zenodo.org/records/2609763/files/dnase_w-120000_r-1000.h5
125690600
md5:3a464a0f820bd969b479920f049fe677
https://zenodo.org/records/2609763/files/dnase_w-12000_r-100.h5
125690600
md5:3c180c3ce233eb1e552fed724d57109f
https://zenodo.org/records/2609763/files/dnase_w-3000_r-25.h5
public
10.1101/597518
Is supplement to
doi
10.5281/zenodo.2609762
isVersionOf
doi