2017-07-12T03:29:06Z https://zenodo.org/oai2d

oai:zenodo.org:232520 2017-01-06T20:17:52Z openaire_data user-greenelab

Way, Gregory 2017-01-06 Dataset is required for a TAD_Pathways analysis (see https://github.com/greenelab/tad_pathways_pipeline). Archived folder includes a TAD based gene index file, curated SNPs from the NHGRI-EBI GWAS catalog, and TAD based genes and SNPs for each GWAS. https://zenodo.org/record/232520 10.5281/zenodo.232520 oai:zenodo.org:232520 doi:10.1101/087718 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ Topologically Associating Domains Genome Wide Association Study Candidate Gene Prioritization Data to initialize a TAD_Pathways Analysis info:eu-repo/semantics/other dataset

oai:zenodo.org:166556 2016-12-13T12:01:21Z software user-greenelab

Way, Gregory Grant, Struan Greene, Casey 2016-11-14 This is a tar archive of the docker image for use in the TAD_pathways analysis pipeline. A less stable but more user friendly version can be downloaded from: https://hub.docker.com/r/gregway/tad_pathways/) To restore the docker image from this archive use the docker load command (https://docs.docker.com/engine/reference/commandline/load/) https://zenodo.org/record/166556 10.5281/zenodo.166556 oai:zenodo.org:166556 doi:10.5281/zenodo.163950 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ Docker Topologically Associating Domains Genome Wide Association Study Bone Mineral Density TAD Pathways Archived Docker Image info:eu-repo/semantics/other software

oai:zenodo.org:163950 2016-12-13T12:01:22Z software user-greenelab

Way, Gregory Greene, Casey 2016-10-31 TAD Pathways analysis for about 300 different traits and diseases - currently outputs TAD based genes for all EBI-NHGRI GWAS catalog traits in replication required journals. https://zenodo.org/record/163950 10.5281/zenodo.163950 oai:zenodo.org:163950 url:https://github.com/greenelab/tad_pathways/tree/v0.1 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/ Topologically Associating Domains Genome Wide Association Studies Gene Prioritization greenelab/tad_pathways: Pre-Release info:eu-repo/semantics/other software

oai:zenodo.org:167467 2016-12-13T12:01:21Z software user-greenelab user-zenodo

Tan, Jie Doing, Georgia Lewis, Kimberley A. Price, Courtney E. Chen, Katheleen M. Cady, Kyle C. Perchuk, Barret Laub, Michael T. Hogan, Deborah A. Greene, Casey S. 2016-11-18 This is the source code required to reproduce data analysis figures from the manuscript, "System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE." This includes the eADAGE method as well as code for the comparison methods. https://zenodo.org/record/167467 10.5281/zenodo.167467 oai:zenodo.org:167467 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause bioinformatics systems biology gene expression denoising autoencoder ensemble eADAGE-1.0.0rc2 info:eu-repo/semantics/other software

oai:zenodo.org:44401 2016-09-12T05:56:55Z user-greenelab software

Casey S. Greene Ailin Song Aaron K. Wong 2016-01-07 This is the version of our analysis code associated with the analyses described in the submission of Song et al. to BioData Mining. https://zenodo.org/record/44401 10.5281/zenodo.44401 oai:zenodo.org:44401 url:https://github.com/greenelab/adni-netwas/tree/v1.0 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause bioinformatics genomics gwas netwas adni-netwas: v1.0 info:eu-repo/semantics/other software

oai:zenodo.org:32851 2016-09-12T05:56:23Z user-greenelab software

Jeffrey A. Thompson Casey S. Greene 2015-10-28 This is the version of the Training Distribution Matching (TDM) analytical code repository that corresponds to the submitted preprint and manuscript. This source code was used to compare TDM to alternative (quantile normalization, log2 transformation) approaches for cross-platform normalization. https://zenodo.org/record/32851 10.5281/zenodo.32851 oai:zenodo.org:32851 doi:10.5281/zenodo.32852 doi:10.5281/zenodo.596066 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause genomics bioinformatics normalization RNA-seq microarray Training Distribution Matching (TDM) Evaluation and Results info:eu-repo/semantics/other software

oai:zenodo.org:30105 2016-09-12T05:56:16Z user-greenelab software

Daniel Himmelstein Casey Greene 2015-09-01 The first release investigates relationships between SNP abundance and network degree. SNP abundance (the number of SNPs in a gene) was calculated for 5 platforms. We visualize relationships with 24 measures of network connectivity. Each measure is the degree (number of edges) for a specific type of network biology edge. https://zenodo.org/record/30105 10.5281/zenodo.30105 oai:zenodo.org:30105 url:https://github.com/dhimmel/snplentiful/tree/v1.0 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/ genotyping sequencing networks biases SNP to gene conversion degree hetnet Highly connected genes contain more SNPs info:eu-repo/semantics/other software

oai:zenodo.org:822470 2017-07-03T19:49:29Z openaire_data user-greenelab

Wong, AK Park, CY Greene, CS Bongo, LA Guan, Y Troyanskaya, OG 2017-07-03 This is the filtered human functional network from the IMP webserver. It was downloaded from http://imp.princeton.edu/download/. https://zenodo.org/record/822470 10.5281/zenodo.822470 oai:zenodo.org:822470 doi:10.1093/nar/gks458 doi:10.5281/zenodo.822469 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ functional network genomics IMP 1.0 Filtered Human Functional Network info:eu-repo/semantics/other dataset

oai:zenodo.org:178613 2016-12-13T12:01:39Z software user-greenelab

Brett Beaulieu-Jones Alex Whan Casey Greene 2016-11-28 This release is associated with the in press version of the continuous analysis manuscript. https://zenodo.org/record/178613 10.5281/zenodo.178613 oai:zenodo.org:178613 url:https://github.com/greenelab/continuous_analysis/tree/v1.0 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause bioinformatics reproducibility greenelab/continuous_analysis: Continuous Analysis v1.0 info:eu-repo/semantics/other software

oai:zenodo.org:34430 2016-09-12T05:56:27Z user-greenelab software

Casey Greene Robert Allaway Balint Kacsoh 2015-11-30 Data and analytical code for the analysis of in vitro flourescence and PDX growth rate data from "Genomic characterization of patient-derived xenograft models established from fine needle aspirate biopsies of a primary pancreatic ductal adenocarcinoma and from patient-matched metastatic sites" by Allaway et al. https://zenodo.org/record/34430 10.5281/zenodo.34430 oai:zenodo.org:34430 url:https://bitbucket.org/greenelab/pdx-dina-manuscript-code/get/aa6f888c0f57.zip info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause genomics bioinformatics patient-derived xenograft Data and analytical code for in vitro and PDX analysis info:eu-repo/semantics/other software

oai:zenodo.org:46165 2016-09-12T05:57:00Z user-greenelab user-zenodo software

Brett Beaulieu-Jones 2016-02-17 No description provided. https://zenodo.org/record/46165 10.5281/zenodo.46165 oai:zenodo.org:46165 url:https://github.com/greenelab/DAPS/tree/0.2 doi:10.5281/zenodo.596032 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause phenotype denoising autoencoders biomedical informatics Denoising Autoencoders for Phenotype Stratification (DAPS): Preprint Release info:eu-repo/semantics/other software

oai:zenodo.org:195238 2016-12-13T12:01:40Z software user-greenelab

Way, Gregory Greene, Casey 2016-12-07 Pipeline steps working. Minting DOI https://zenodo.org/record/195238 10.5281/zenodo.195238 oai:zenodo.org:195238 url:https://github.com/greenelab/gbm_immune_validation/tree/0.01 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause greenelab/gbm_immune_validation: Initial Release info:eu-repo/semantics/other software

oai:zenodo.org:158947 2016-12-13T12:01:39Z software user-greenelab

Tan, Jie Doing, Georgia Lewis, Kimberley A. Price, Courtney E. Chen, Katheleen M. Cady, Kyle C. Perchuk, Barret Laub, Michael T. Hogan, Deborah A. Greene, Casey S. 2016-09-29 This is the source code required to reproduce data analysis figures from the initial preprint for, "System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE." This includes the eADAGE method as well as code for the comparison methods. https://zenodo.org/record/158947 10.5281/zenodo.158947 oai:zenodo.org:158947 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause bioinformatics systems biology gene expression denoising autoencoder ensemble eADAGE-1.0.0rc1 info:eu-repo/semantics/other software

oai:zenodo.org:580093 2017-05-15T18:02:20Z software user-greenelab

Tan, Jie Doing, Georgia Lewis, Kimberley A Price, Courtney E Chen, Kathleen M. Cady, Kyle C. Perchuk, Barret Laub, Michael T. Hogan, Deborah A. Greene, Casey S. 2017-05-15 This is the source code required to reproduce data analysis figures from the manuscript, "System-wide automatic extraction of functional signatures in Pseudomonas aeruginosa with eADAGE." This includes the eADAGE method as well as code for the comparison methods. In addition to the bitbucket repository, five files have been added. One is a readme describing the files added for zenodo. The others are the Pseudomonas aeruginosa compendium used in this work, the weight matrices of the eADAGE model, the signatures from the eADAGE model, and the activity in each sample of the eADAGE model nodes. https://zenodo.org/record/580093 10.5281/zenodo.580093 oai:zenodo.org:580093 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/4.0/ gene expression bioinformatics unsupervised ADAGE Pseudomonas aeruginosa eADAGE-1.0.0 info:eu-repo/semantics/other software

oai:zenodo.org:33146 2016-09-12T05:56:24Z user-greenelab software

Jie Tan Casey S. Greene 2015-11-03 This is the first release of the code in support of the manuscript "ADAGE-based analysis of publicly available gene expression data collections illuminates Pseudomonas aeruginosa-host interactions" (submitted). https://zenodo.org/record/33146 10.5281/zenodo.33146 oai:zenodo.org:33146 url:https://github.com/greenelab/adage/tree/v0.9 doi:10.5281/zenodo.596070 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause ADAGE genomics unsupervised gene expression ADAGE: Analysis using Denoising Autoencoders of Gene Expression info:eu-repo/semantics/other software

oai:zenodo.org:32906 2016-09-12T05:56:25Z user-greenelab software

Gregory Way James Rudd Casey Greene 2015-10-29 Analytical code to accompany the manuscript: "High-grade serous ovarian cancer subtypes are similar across populations" https://zenodo.org/record/32906 10.5281/zenodo.32906 oai:zenodo.org:32906 url:https://github.com/greenelab/hgsc_subtypes/tree/1.1.1 doi:10.5281/zenodo.596048 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause genomics ovarian cancer molecular subtype unsupervised clustering Analytical Code for "Cross-population analysis of high-grade serous ovarian cancer reveals only two robust subtypes" info:eu-repo/semantics/other software

oai:zenodo.org:32852 2016-09-12T05:56:24Z user-greenelab software

Jeffrey A. Thompson Casey S. Greene 2015-10-28 This R package implements Training Distribution Matching (TDM) as described in Thompson et al. (submitted). TDM is a normalization technique that allows machine learning models built for one platform for gene expression measurement (e.g. microarrays) to be applied to a different platform (e.g RNA-sequencing). The companion repository (see "related") provides analytical code used to evaluate this method. https://zenodo.org/record/32852 10.5281/zenodo.32852 oai:zenodo.org:32852 doi:10.5281/zenodo.32851 info:eu-repo/semantics/openAccess http://www.opensource.org/licenses/BSD-3-Clause genomics bioinformatics normalization cross-platform RNA-seq microarray Training Distribution Matching (TDM) R Package info:eu-repo/semantics/other software

oai:zenodo.org:44668 2016-09-12T05:56:55Z user-greenelab software

Jeffrey A. Thompson Casey S. Greene 2016-01-13 Scripts and data for re-creating TDM results. https://zenodo.org/record/44668 10.5281/zenodo.44668 oai:zenodo.org:44668 url:https://github.com/greenelab/TDMresults/tree/v1.0.0 doi:10.5281/zenodo.596066 info:eu-repo/semantics/openAccess Training Distribution Matching (TDM) Results: Analysis Code for Accepted TDM Manuscript info:eu-repo/semantics/other software

oai:zenodo.org:824139 2017-07-07T15:49:31Z software user-greenelab

Way, Gregory Greene, Casey 2017-07-07 This release focuses on analyses and summary figures for training and evaluating a Ras classifier as part of the Ras/NF1 TCGA analysis group. https://zenodo.org/record/824139 10.5281/zenodo.824139 oai:zenodo.org:824139 url:https://github.com/greenelab/pancancer/tree/v2.0 doi:10.5281/zenodo.596933 info:eu-repo/semantics/openAccess The Cancer Genome Atlas Ras Pathway Machine Learning Cancer Gene Expression greenelab/pancancer: Ras Pathway Hyperactivation Classifier info:eu-repo/semantics/other software