cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.1346215
title: Cross-Tissue Eqtl Enrichment Of Associations In Schizophrenia

description: non-CNS data used in the study.

the original data these were generated from have been deposited in the European Genome-phenome Archive (EGA) under accession EGAS00001000805.

complete files (all associations):<br>
org/blood_cis_all.gz (whole blood)<br>
org/fat_cis_all.gz (adipose)<br>
org/lcl_all_cis.gz (LCLs)<br>
org/skin_cis_all.gz (epidermal)

e-gene files (best association per gene at FDR &lt; 0.01):<br>
org/eQTL.B.Peer50.FDR01 (whole blood)<br>
org/eQTL.F.Peer50.FDR01 (adipose)<br>
org/eQTL.L.Peer50.FDR01 (LCLs)<br>
org/eQTL.S.Peer50.FDR01 (epidermal)

control variants (2m template) bed files:<br>
fakeQTL_tw_blood.bed<br>
fakeQTL_tw_fat.bed<br>
fakeQTL_tw_lcl.bed<br>
fakeQTL_tw_skin.bed

control variants (2m template) rs names:<br>
fakeQTL_tw_blood.mrk<br>
fakeQTL_tw_fat.mrk<br>
fakeQTL_tw_lcl.mrk<br>
fakeQTL_tw_skin.mrk

control variants (9m template) R data files:<br>
fakeQTL9m_tw_blood.RData<br>
fakeQTL9m_tw_fat.RData<br>
fakeQTL9m_tw_lcl.RData<br>
fakeQTL9m_tw_skin.RData

control variants (9m template) matlab files:<br>
fakeQTL9m_tw_blood.mat<br>
fakeQTL9m_tw_fat.mat<br>
fakeQTL9m_tw_lcl.mat<br>
fakeQTL9m_tw_skin.mat

 

if you use these data, please cite the data sources:

Genetic interactions affecting human gene expression identified by variance association mapping. Brown, A.A., Buil, A., Viñuela, A., Lappalainen, T., Zheng, H.-F., Richards, J.B., Small, K.S., Spector, T.D., Dermitzakis, E.T. and Durbin, R. (2014). eLife 2014;3:e01381 doi: 10.7554/eLife.01381

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Buil, A., Brown, A.A., Lappalainen, T., Vinuela, A., Davies, M.N., Zheng, H.-F., Richards, J.B., Glass, D., Small, K.S., Durbin, R. et al. (2015) Nat Genet, 47, 88-91.
DOI: 10.23725/3tvs-js06
title: NWD146103.recab.cram.crai

description: TOPMed: NWD146103 <br>HapMap_1000G: NA19238 <br>Seq Ctr: WashU <br>File:  CRAI index file
DOI: 10.25919/5b752ad7b5763
title: Parkes observations for project P892 semester 2018APRS_07

description: SUPERBx looks at the highest Galactic latitudes in a search for pulsars and fast radio bursts (FRBs). We use optimised GPU codes and supercomputing to search for these, making discoveries in real time. Handling our data as it comes in is essential for the SKA Phase I era so this work applies directly to the high-data rates of next generation telescopes. Our pulsar discoveries are typically nearby scintillating sources, intermittent sources and those in interesting binary systems. Our FRB discoveries have discovery lags of ~1 second, rather than months/years and these feed rapid alerts to the world-wide follow-up community via a dedicated VOEvent format an Astronomer's Telegrams. The goal of this is to allow localisation of the discovered FRBs. This is key for identifying FRB host galaxies, so as to solve the mystery of their progenitors and to exploit their many uses as tools for precision cosmology measurements.
DOI: 10.3886/e105261v2-7782
title: HIV retention at selected facilities in Namayingo district, Eastern Uganda

description: In Namayingo district, Eastern Uganda, HIV prevalence is above national Level. <br><br>Consequently, many HIV interventions have been scaled up in this district to curb down HIV transmission. However, HIV retention rate plays a big role in realising the target of HIV transmission reduction. Knowledge of HIV retention among HIV patients in Namayingo district is key in fueling up the up-scaling of HIV transmission-targeted interventions.<br><br>So these data pertain to variables of HIV retention, and other factors associated with it.
DOI: 10.5281/zenodo.1346303
title: Test Data For Running Snakepipes : Dna-Mapping Workflow

description: <strong>Test files for running snakePipes workflows</strong>

<strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to this link for further information on snakePipes.

This folder contains test files that can be used to run DNA-mapping workflow under snakePipes. To test the workflow, follow the following steps : 


	Download or prepare genome fasta, indices and annotations for human (<strong>hg38</strong>) genome.
	Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`
	Update Genome configuration file with path to indices and annotations.
	Move to this repository and run the example <strong>command.sh</strong>
DOI: 10.23725/a9pq-r198
title: NWD155824.recab.cram

description: TOPMed: NWD155824 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAM file
DOI: 10.5065/d6v69hdr
title: IGAC/SPARC Chemistry-Climate Model Initiative (CCMI) Community Simulations in Support of Upcoming Ozone and Climate Assessments

description: Output are from the CESM2(WACCM-X).The model’s dynamical fields (temperature, zonal and meridional winds and surface pressure) are specified in the troposphere and stratosphere from the Modern Era Retrospective Analysis for Research and Applications (MERRA) [Rienecker et al., 2011]. The model has a horizontal resolution of 1.9˚ latitude by 2.5˚ longitude. This simulation followed the “REFC1D” protocol of the Chemistry Climate Model Initiative [Eyring et al., 2013] for the specification of time-dependent greenhouse gases and ozone depleting substances. Data are provided for evaluation/validation purposes. Please contact marsh@ucar.edu for terms of use.

Eyring et al. (2013), Overview of IGAC/SPARC Chemistry-Climate Model Initiative (CCMI) Community Simulations in Support of Upcoming Ozone and Climate Assessments, SPARC newsletter, Zurich, Switzerland, 40, 48–66.

Rienecker, M. M., et al. (2011), MERRA: NASA’s Modern-Era Retrospective Analysis for Research and Applications, J. Clim., 24, 3624–3648, doi:10.1175/JCLI-D- 11-00015.1

Daily average data includes ordinary daily averages (h3) and daily average​s of ​transformed Eulerian mean zonal mean​ (h5)
DOI: 10.23725/q3rr-cf79
title: NWD155824.recab.cram.crai

description: TOPMed: NWD155824 <br>HapMap_1000G: NA12878 <br>Seq Ctr: Broad <br>File:  CRAI index file
DOI: 10.3886/e105440v3
title: Explaining the Declines in US Rural Mortality

description: Data includes: (1) mortality from the U.S. Vital Statistics for all states outside of the Northeast. (2) County Health Department data from the History of County Health Organizations in the United States. (3) Taxation data from U.S. Wealth, Debt and Taxation entries. (4) The controls from computed summary statistics of the IPUMS Restricted Complete Count Data.
DOI: 10.5517/ccdc.csd.cc20hx6n
title: CCDC 1862331: Experimental Crystal Structure Determination

description: Related Article: Brian W. Skelton, George A. Koutsantonis, Campbell F.R. MacKenzie|2018|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.17632/5226rtjtwc.1
title: A Mathematical Model for Optimizing Port Terminals with Several Types of Machines (Tests and Codes)

description: Tests, Results aand Codes of the paper "A Mathematical Model for Optimizing Port Terminals with Several Types of Machines"
DOI: 10.23725/8na3-9s47
title: NWD165827.recab.cram

description: TOPMed: NWD165827 <br>HapMap_1000G: NA19238 <br>Seq Ctr: UW <br>File:  CRAM file
DOI: 10.17632/5frzx86whr.1
title: Humor in sport psychology consultancy

description: Survey relating to use of humor in applied sport psychology.
DOI: 10.17632/5jc2fxgvrv.1
title: Humor in Sport Psychology Consulting

description: Humor in Sport Psychology Consulting - Quantitative survey.
DOI: 10.17632/9gh2tmtnph.1
title: Data for: Board Meeting Frequency and Firm Performance: Examining the Nexus in Nigerian Deposit Money Banks

description: This the summary of the data set used for the manuscript tilted: Board Meeting Frequency and Firm Performance: Examining the Nexus in Nigerian Deposit Money Banks
DOI: 10.23725/2g4s-qv04
title: NWD165827.recab.cram.crai

description: TOPMed: NWD165827 <br>HapMap_1000G: NA19238 <br>Seq Ctr: UW <br>File:  CRAI index file
DOI: 10.5281/zenodo.1345775
title: Supplemental Materials to Accompany: Abowd and Schmutte "An Economic Analysis of Privacy Protection and Statistical Accuracy as Social Choices"

description: Materials to supplement "An Economic Analysis of Privacy Protection and Statistical Accuracy as Social Choices" by John Abowd and Ian Schmutte.
description: Supported by:
Alfred P. Sloan Foundation Grant G-2015-13903;
NSF Grants SES-1131848, BCS-0941226, TC-1012593;
 EPSRC Grant no. EP/K032208/1
DOI: 10.15129/eca751cb-8c6d-46b7-a8b0-13133e8e2526
title: Data for: "Ratiometric Raman imaging reveals the new anti-cancer potential of lipid targeting drugs"

description: This data was generated for the publication of a research article with the same title and investigates the effect of a number of drugs targeting lipid metabolism on cellular lipid levels as potential anti-cancer agents using Raman spectroscopy. Raman data was taken using a Renishaw inVia system with Renishaw Wire 4.1 software and is provided in .wdf format as raw data and post processing in Wire 4.1 as well as in .spc format post processing. Live dead staining images were captured on a Nikon Eclipse LV100 microscope with a Photometrics CoolSNAP and images are provided as raw .tif files and processed .jpg files. Fluorescence images for phospholipidosis and steatosis staining were captured on a Leica Microsystems SP8 confocal microscope with LASX software and images are provided in a .lif file and as exported .jpg. 

[This is a place-holder record. Active DOI will be minted & data made public on publication of related research output - Data made public and active DOI minted 17/08/18]
DOI: 10.25919/5b7536063537f
title: Parkes observations for project P456 semester 2018APRS_11

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. The PPTA is the oldest of three international pulsar timing groups. We have the smallest telescope and the smallest group, but the best measurements and the best results. Our bound on the strength of the incoherent gravitational wave background is the only bound which significantly constrains theoretical models. We have maintained our leading position because: we have the southern sky; we have a small but well-focussed group; we have the best-calibrated receivers; and we have been able to observe with an almost regular cadence of 15 to 20 days at three different wavelengths. With this proposal we aim to maintain our pre-eminent position in the field.

Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.5281/zenodo.1343364
title: Human Peroxisomal Coenzyme A Diphosphatase (Nudt7); A Target Enabling Package

description: In an effort to characterise the human NUDIX family SGC Oxford has expressed recombinant human NUDT7 as part of the SGC chemical probe programme and solved the first crystal structure of this enzyme. This enabled a crystallographic fragment screen which in conjunction with a separate covalent fragment approach yielded a first-in-class small molecule inhibitor of NUDT7 with activity in the single-digit micromolar range in a catalytic assay. This compound paves the way for chemical probe development and further functional exploration of NUDT7 in physiological and disease contexts.
description: Future versions of this document will contain experimental data on the NUDT7 TEP.
DOI: 10.5281/zenodo.1346283
title: Detection Of Genetic Alterations In Gastric Cancer Patients From Saudi Arabia Using Comparative Genomic Hybridization (Cgh)

description: Abstract

Background: The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population. 

Methods: Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip. 

Results: Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.
DOI: 10.5517/ccdc.csd.cc1jcng0
title: CCDC 1411382: Experimental Crystal Structure Determination

description: Related Article: Andrew C. Behrle, Alexander J. Myers, Andrew Kerridge, Justin R. Walensky|2018|Inorg.Chem.|57|10518|doi:10.1021/acs.inorgchem.8b00077
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1jcnh1
title: CCDC 1411383: Experimental Crystal Structure Determination

description: Related Article: Andrew C. Behrle, Alexander J. Myers, Andrew Kerridge, Justin R. Walensky|2018|Inorg.Chem.|57|10518|doi:10.1021/acs.inorgchem.8b00077
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d3j
title: CCDC 1587947: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d2h
title: CCDC 1587946: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d4k
title: CCDC 1587948: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d5l
title: CCDC 1587949: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d6m
title: CCDC 1587950: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d7n
title: CCDC 1587951: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1q9d8p
title: CCDC 1587952: Experimental Crystal Structure Determination

description: Related Article: Ying Lü, Xiao Zhang, Xiao-Bing Cui, Ji-Qing Xu|2018|Inorg.Chem.|57|11123|doi:10.1021/acs.inorgchem.8b01705
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc1zwjq3
title: CCDC 1843716: Experimental Crystal Structure Determination

description: Related Article: Evanta Kabir, Dhruti Patel, Kevin Clark, Thomas S. Teets|2018|Inorg.Chem.|57|10906|doi:10.1021/acs.inorgchem.8b01543
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.14457/mu.the.2015.276
title: Graduate trpombone recital
DOI: 10.17632/b4mxg7ydb7.1
title: Android permissions dataset

description: This dataset consists of apps needed permissions during installation and run-time. We collect apps from three different sources google play, third-party apps and malware dataset.
DOI: 10.17632/fjn2dtckvh.1
title: RH readout Characterization

description: Humidity sensor system ADC output characterization recorded Vs relative humidity level
DOI: 10.5065/d6qf8rqg
title: IGAC/SPARC Chemistry-Climate Model Initiative (CCMI) Community Simulations in Support of Upcoming Ozone and Climate Assessments

description: Output are from the CESM2(WACCM-X 2.0). These are results from a free running historical simulation. The model has a horizontal resolution of 1.9˚ latitude by 2.5˚ longitude. This simulation followed the “REFC1D” protocol of the Chemistry Climate Model Initiative [Eyring et al., 2013] for the specification of time-dependent greenhouse gases and ozone depleting substances. Data are provided for evaluation/validation purposes. Please contact marsh@ucar.edu for terms of use.

Eyring et al. (2013), Overview of IGAC/SPARC Chemistry-Climate Model Initiative (CCMI) Community Simulations in Support of Upcoming Ozone and Climate Assessments, SPARC newsletter, Zurich, Switzerland, 40, 48–66.

Daily average data includes ordinary daily averages (h3) and daily average​s of ​transformed Eulerian mean zonal mean​ (h5)
DOI: 10.5281/zenodo.1345741
title: Predicted Human Immunopeptidome

description: Comprehensive peptide-MHC binding predictions were performed for all 8-11mer peptides in the human proteome to all class I MHC available for prediction using NetMHCpan 3.0.

human_immunopeptidome_files.tar.gz, when decompressed, contains a directory of all individual HLA files each containing all self-peptides predicted to bind. Alternatively, if only a subset of HLA alleles are of interest to you, decompressed individual files are available for each HLA. Note that these are identical to the files contained within the .tar.gz archive file.

Details on the creation of this dataset can be found here: https://github.com/scottdbrown/self-immunopeptidome_cancer
DOI: 10.5281/zenodo.1345742
title: Predicted Human Immunopeptidome

description: Comprehensive peptide-MHC binding predictions were performed for all 8-11mer peptides in the human proteome to all class I MHC available for prediction using NetMHCpan 3.0.

All binding peptide-MHC pairs (IC<sub>50</sub> &lt; 500 nM) are listed in this dataset.

Details on the creation of this dataset can be found here: https://github.com/scottdbrown/self-immunopeptidome_cancer