cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7091474.v1
title: Additional file 1: of Association between semi-quantitative microbial load and respiratory symptoms among Thai military recruits: a prospective cohort study

description: Dataset. Title of data: Semi-quantitative microbial load in throat and nasal swab samples from Thai Army recruits. Description of data: Semi-quantitative microbial load in non-acute and acute throat and nasal swab samples from Thai Army recruits, determined using a commercial multiplex real-time PCR assay comprising 33 bacterial, viral and fungal targets; includes names, labels, and coding for individual variables. (XLS 311 kb)
DOI: 10.6084/m9.figshare.7091462
title: Additional file 11: of Cryptic sequence features in the active postmortem transcriptome

description: 11 sheets in MS Excel file. It is similar to the Online Resource_9 mouse file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 69035 kb)
DOI: 10.6084/m9.figshare.7091462.v1
title: Additional file 11: of Cryptic sequence features in the active postmortem transcriptome

description: 11 sheets in MS Excel file. It is similar to the Online Resource_9 mouse file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 69035 kb)
DOI: 10.6084/m9.figshare.7091450
title: Additional file 6: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S16. BRCA1/2 LOH calls using different LOH calling approaches. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.7091447
title: Additional file 10: of Cryptic sequence features in the active postmortem transcriptome

description: 11 sheets in MS Excel file. It is similar to the Online Resource_8 zebrafish file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 65834 kb)
DOI: 10.6084/m9.figshare.7091447.v1
title: Additional file 10: of Cryptic sequence features in the active postmortem transcriptome

description: 11 sheets in MS Excel file. It is similar to the Online Resource_8 zebrafish file except the raw data is missing to reduce matrix size. The purpose of the sheets is to calculate over- and under-abundant mers that are 5 X the standard deviation of the CP for each mer. The first sheet provides a detailed Readme that describes the sheets. Rows differ by mer length. (XLSX 65834 kb)
DOI: 10.6084/m9.figshare.7091450.v1
title: Additional file 6: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S16. BRCA1/2 LOH calls using different LOH calling approaches. (XLS 51Â kb)
DOI: 10.6084/m9.figshare.7091435
title: Additional file 5: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S4. List of ClinVar, IARC-TP53, and CADD damaging germline variants used. (XLS 836Â kb)
DOI: 10.6084/m9.figshare.7091435.v1
title: Additional file 5: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S4. List of ClinVar, IARC-TP53, and CADD damaging germline variants used. (XLS 836Â kb)
DOI: 10.6084/m9.figshare.7091426
title: Additional file 4: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S3. Gene-level frequency of mono- and bi-allelic germline alterations. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.7091426.v1
title: Additional file 4: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S3. Gene-level frequency of mono- and bi-allelic germline alterations. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.7091417
title: MOESM3 of Secular and coseismic changes in S-wave velocity detected using ACROSS in the Tokai region

description: Additional file 3. Secular and coseismic change for each station.
DOI: 10.6084/m9.figshare.7091414
title: Additional file 3: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S2. List of genes and pathways used. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.7091414.v1
title: Additional file 3: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S2. List of genes and pathways used. (XLS 27Â kb)
DOI: 10.6084/m9.figshare.7091399
title: MOESM2 of Secular and coseismic changes in S-wave velocity detected using ACROSS in the Tokai region

description: Additional file 2. Date and amount ofÂ the time shiftÂ corrections at the replacements of data loggers.
DOI: 10.6084/m9.figshare.7091396
title: Additional file 2: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S1. Gene set enrichment analysis on gene-level frequency of bi-allelic alteration. (XLS 90Â kb)
DOI: 10.6084/m9.figshare.7091399.v1
title: MOESM2 of Secular and coseismic changes in S-wave velocity detected using ACROSS in the Tokai region

description: Additional file 2. Date and amount ofÂ the time shiftÂ corrections at the replacements of data loggers.
DOI: 10.6084/m9.figshare.7091396.v1
title: Additional file 2: of Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas

description: Table S1. Gene set enrichment analysis on gene-level frequency of bi-allelic alteration. (XLS 90Â kb)
DOI: 10.6084/m9.figshare.7091390
title: MOESM1 of Secular and coseismic changes in S-wave velocity detected using ACROSS in the Tokai region

description: Additional file 1. Date and amount of the time shiftÂ corrections with Kunitomo (2014)â s method.
DOI: 10.6084/m9.figshare.7091390.v1
title: MOESM1 of Secular and coseismic changes in S-wave velocity detected using ACROSS in the Tokai region

description: Additional file 1. Date and amount of the time shiftÂ corrections with Kunitomo (2014)â s method.
DOI: 10.6084/m9.figshare.7091240
title: MOESM3 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file Â 3. Capture mark recapture with columns representing dates of capture and rows representing individuals.
DOI: 10.6084/m9.figshare.7091240.v1
title: MOESM3 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file Â 3. Capture mark recapture with columns representing dates of capture and rows representing individuals.
DOI: 10.6084/m9.figshare.7091231
title: MOESM2 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file 2. The swab results of all species except Acris crepitans.
DOI: 10.6084/m9.figshare.7091225
title: MOESM1 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file 1. Capture details for each Acris crepitans captured in the study.
DOI: 10.6084/m9.figshare.7091231.v1
title: MOESM2 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file 2. The swab results of all species except Acris crepitans.
DOI: 10.6084/m9.figshare.7091225.v1
title: MOESM1 of Fungal infection has sublethal effects in a lowland subtropical amphibian population

description: Additional file 1. Capture details for each Acris crepitans captured in the study.
DOI: 10.6084/m9.figshare.7091198
title: Additional file 6 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 1 and we use the ML topology. The file is compressed in gzip format. (GZ 8293 kb)
DOI: 10.6084/m9.figshare.7091198.v1
title: Additional file 6 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 1 and we use the ML topology. The file is compressed in gzip format. (GZ 8293 kb)
DOI: 10.6084/m9.figshare.7091186
title: Additional file 5 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 1 and we use the MAP topology. The file is compressed in gzip format. (GZ 8412 kb)
DOI: 10.6084/m9.figshare.7091186.v1
title: Additional file 5 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 1 and we use the MAP topology. The file is compressed in gzip format. (GZ 8412 kb)
DOI: 10.6084/m9.figshare.7091180
title: Additional file 4 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 10 and we use the ML topology. The file is compressed in gzip format. (GZ 8151 kb)
DOI: 10.6084/m9.figshare.7091180.v1
title: Additional file 4 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 10 and we use the ML topology. The file is compressed in gzip format. (GZ 8151 kb)
DOI: 10.6084/m9.figshare.7091165
title: Additional file 3 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 10 and we use the MAP topology. The file is compressed in gzip format. (GZ 8365 kb)
DOI: 10.6084/m9.figshare.7091165.v1
title: Additional file 3 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 10 and we use the MAP topology. The file is compressed in gzip format. (GZ 8365 kb)
DOI: 10.6084/m9.figshare.7091156
title: Additional file 2 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 100 and we use the ML topology. The file is compressed in gzip format. (GZ 7658 kb)
DOI: 10.6084/m9.figshare.7091156.v1
title: Additional file 2 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 100 and we use the ML topology. The file is compressed in gzip format. (GZ 7658 kb)
DOI: 10.6084/m9.figshare.7091150
title: Additional file 1 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 100 and we use the MAP topology. The file is compressed in gzip format. (GZ 8234 kb)
DOI: 10.6084/m9.figshare.7091150.v1
title: Additional file 1 of DM-PhyClus: a Bayesian phylogenetic algorithm for infectious disease transmission cluster inference

description: This file contains an R object giving the results for the scenario in the simulation study where the concentration parameter prior is assumed to have mean 100 and we use the MAP topology. The file is compressed in gzip format. (GZ 8234 kb)
DOI: 10.6084/m9.figshare.7091141
title: Additional file 1 of Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd

description: All source codes and the solutions obtained by GridProd in the computational experiments described in this manuscript are included. (ZIP 2373 kb)
DOI: 10.6084/m9.figshare.7091078
title: GeoODK_Carrasco-Escobar2018 Metadata

description: Metadata collected with GeoODK
DOI: 10.6084/m9.figshare.7091141.v1
title: Additional file 1 of Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd

description: All source codes and the solutions obtained by GridProd in the computational experiments described in this manuscript are included. (ZIP 2373 kb)
DOI: 10.6084/m9.figshare.7091075
title: GeoODK_Carrasco-Escobar2018 Shapefile

description: Shapefile of raw data from GeoODK
DOI: 10.6084/m9.figshare.7091078.v1
title: GeoODK_Carrasco-Escobar2018 Metadata

description: Metadata collected with GeoODK
DOI: 10.6084/m9.figshare.7091057
title: Normalized genomic data for survival prediction in oligodendrogliomas

description: This files contains overall survival and normalized genomic features for TCGA oligodendrogliomas (defined as having mutations in IDH1/IDH2 and co-deletion of chromosomes 1p and 19q).<br>This data was utilized in machine learning prediction of survival for the paper "<i>Multi-faceted computational assessment of risk and progression in oligodendroglioma uncovers crucial role of Notch and PI3K pathways"</i> in Nature Precision Oncology (in press).
DOI: 10.6084/m9.figshare.7091057.v1
title: Normalized genomic data for survival prediction in oligodendrogliomas

description: This files contains overall survival and normalized genomic features for TCGA oligodendrogliomas (defined as having mutations in IDH1/IDH2 and co-deletion of chromosomes 1p and 19q).<br>This data was utilized in machine learning prediction of survival for the paper "<i>Multi-faceted computational assessment of risk and progression in oligodendroglioma uncovers crucial role of Notch and PI3K pathways"</i> in Nature Precision Oncology (in press).
DOI: 10.6084/m9.figshare.7091003
title: Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

description: Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'<br><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (MMETSP_all_evaluation_matrix.csv)<b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (MMETSP_all_evaluation_matrix_METADATA.csv)<b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb, .html)<b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipyn, .html)<b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)<b>Supplemental Figure 2:</b> Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf)<b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)<b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .ipynb)<br>Other notebooks (all .html) used to generate Figures for Johnson et al 2018:<br>Johnson_etal_2018_GigaScience_Figures.ipynbFigures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynbFigure8_aov.ipynbMMETSP_transcriptome_assembly_stats.ipynbmake_large_assembly_evaluation_matrix.ipynb<br>Files located on GitHub:<br>https://github.com/ljcohen/MMETSP
DOI: 10.6084/m9.figshare.7091027.v1
title: Maintien de la paix de l’ONU avec participation hongroise: Namibie

description: Au cours des dernières années les specialistes du maintien de la paix et des gens qui ne sont pas du métier peuvent obtenir des informations sur les operations policières et militaires de maintien de paix de la Republique de Hongrie en afrique.Pourtant, il y a quand même des évenements dont on ne s’occupe pratiquement pas ou peu. Dans l’article suivant nous traiterons la Namibie, du rôle des opérations policières hongroises dans ce pays.
DOI: 10.6084/m9.figshare.7091003.v1
title: Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

description: Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'<br><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (.csv)<b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (.csv)<b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb)<b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipynb)<b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf and .docx)<b>Supplemental Figure 2:</b> Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf and .docx)<b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf and .docx)<b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .docx and .ipynb)<br>Other notebooks used to generate Figures for Johnson et al 2018:<br>Johnson_etal_2018_GigaScience_Figures.ipynbFigures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynbFigure8_aov.ipynbMMETSP_transcriptome_assembly_stats.ipynbmake_large_assembly_evaluation_matrix.ipynb<br>Files located on GitHub:https://github.com/ljcohen/MMETSP
DOI: 10.6084/m9.figshare.7091003.v2
title: Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

description: Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'<br><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (.csv)<b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (.csv)<b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb)<b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipynb)<b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)<b>Supplemental Figure 2:</b> Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf)<b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)<b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .ipynb)<br>Other notebooks used to generate Figures for Johnson et al 2018:<br>Johnson_etal_2018_GigaScience_Figures.ipynbFigures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynbFigure8_aov.ipynbMMETSP_transcriptome_assembly_stats.ipynbmake_large_assembly_evaluation_matrix.ipynb<br>Files located on GitHub:https://github.com/ljcohen/MMETSP
DOI: 10.6084/m9.figshare.7090697
title: Kraken (v1) Accuracy dataset

description: Wood et al simulated dataset used to evaluate the accuracy of Kraken v1 (and other classifiers) in the original Kraken publication; contains three FASTA files and instructions for obtaining the source taxonomic IDs for each sequence. These simulated metagenomic samples (each 10,000 reads) were also used to evaluate the speed of the non-Kraken classifiers.
DOI: 10.6084/m9.figshare.7090697.v1
title: Kraken (v1) Accuracy dataset

description: Wood et al simulated dataset used to evaluate the accuracy of Kraken v1 (and other classifiers) in the original Kraken publication; contains three FASTA files and instructions for obtaining the source taxonomic IDs for each sequence. These simulated metagenomic samples (each 10,000 reads) were also used to evaluate the speed of the non-Kraken classifiers.
DOI: 10.6084/m9.figshare.7091003.v3
title: Supplemental Information for MMETSP article: 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'

description: Supplemental Information for the MMETSP article, 'Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes'<br><b>Supplemental Table 1:</b> All evaluation metrics collected for Johnson et al. 2018 (MMETSP_all_evaluation_matrix.csv)<b>Supplemental Table 2:</b> Metadata for Supplemental Table 1 (MMETSP_all_evaluation_matrix_METADATA.csv)<b>Supplemental Notebook 1:</b> comparison between NCBI SRA and iMicrobe sample information (.ipynb)<b>Supplemental Notebook 2:</b> Trinity version comparisons (.ipynb)<b>Supplemental Figure 1:</b> Transrate score comparisons between DIB re-assemblies and the two 'cds' and 'nt' versions of the NCGR assemblies (.pdf)<b>Supplemental Figure 2:</b> Frequency distribution of differences between Transrate scores between the NCGR ‘nt’ assemblies and the DIB re-assemblies grouped by the top seven most represented phyla in the MMETSP data set (.pdf)<b>Supplemental Figure 3:</b> The mean proportion of contigs with complete protistan universal single copy orthologs (BUSCO) recovered in each assembly (.pdf)<b>Supplemental Figure 4:</b> A subset of MMETSP samples. (.pdf and .ipynb)<br>Other notebooks used to generate Figures for Johnson et al 2018:<br>Johnson_etal_2018_GigaScience_Figures.ipynbFigures 4 and 7 - MMETSP_unique_kmers_dammitgenenames.ipynbFigure8_aov.ipynbMMETSP_transcriptome_assembly_stats.ipynbmake_large_assembly_evaluation_matrix.ipynb<br>Files located on GitHub:https://github.com/ljcohen/MMETSP
DOI: 10.6084/m9.figshare.7090634
title: Test Dataset

description: Simple test dataset used for independently verifying the fetch_external_dataset() function in the matminer package<br>
DOI: 10.6084/m9.figshare.7090634.v1
title: Test Dataset

description: Simple test dataset used for independently verifying the fetch_external_dataset() function in the matminer package<br>
DOI: 10.6084/m9.figshare.7090568
title: Supplemental tables

description: Supplemental tables for the associated manuscript
DOI: 10.6084/m9.figshare.7090568.v1
title: Supplemental tables

description: Supplemental tables for the associated manuscript