cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c377tq8/2
title: Aliyu_2017_Biotropica_CarapaCondMut_CODE_Phenology_LargeSeededSpecies

description: Code to plot the phenology data in the file: Aliyu_2017_Biotropica_CarapaCondMut_DATA_Phenology_LargeSeededSpecies.csv
DOI: 10.5061/dryad.c377tq8/3
title: Aliyu_2017_Biotropica_CarapaCondMut_DATA_SeedFates

description: Seed fate data for the main experiment and analyses.
DOI: 10.5061/dryad.dp8b07r/10
title: Sub10
DOI: 10.5061/dryad.dp8b07r/11
title: Sub11
DOI: 10.5061/dryad.dp8b07r/12
title: Sub12
DOI: 10.5061/dryad.dp8b07r/13
title: Sub13
DOI: 10.5061/dryad.dp8b07r/14
title: Sub14
DOI: 10.5061/dryad.dp8b07r/6
title: Sub06
DOI: 10.5061/dryad.dp8b07r/7
title: Sub07
DOI: 10.5061/dryad.dp8b07r/8
title: Sub08
DOI: 10.5061/dryad.dp8b07r/9
title: Sub09
DOI: 10.5061/dryad.kc7h9.1
title: Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome
DOI: 10.5061/dryad.kc7h9.1/1.1
title: trnL data set

description: This file contains trnL data with metadata. The trnL data have been processed as described in Metcalf et al. 2017.
DOI: 10.5061/dryad.kc7h9.1/2.1
title: Diet.Matrix.taxonomy

description: Taxonomy strings assigned to trnL sequences. Taxonomy could not be assigned to most sequences.
DOI: 10.5061/dryad.kc7h9.2
title: Data from: Evaluating the impact of domestication and captivity on the horse gut microbiome
DOI: 10.5061/dryad.kc7h9.2/1.2
title: trnL data set

description: This file contains trnL data with metadata. The trnL data have been processed as described in Metcalf et al. 2017.
DOI: 10.5061/dryad.kc7h9.2/2.2
title: Diet.Matrix.taxonomy

description: Taxonomy strings assigned to trnL sequences. Taxonomy could not be assigned to most sequences.
DOI: 10.5061/dryad.kc7h9.2/3.2
title: Sample metadata, Supplementary Table 3
DOI: 10.5061/dryad.pq0cs6h/1
title: cohorts

description: Cohort descriptions used to evaluate and train the L-PCRS system.
DOI: 10.5061/dryad.pq0cs6h/2
title: judgments

description: Relevance judgments used to train and evaluate the L-PCRS system.
DOI: 10.5061/dryad.pq0cs6h/3
title: trained_models

description: Random Forest classifiers trained on each dataset, in Lemur's RankLib.jar format.
DOI: 10.5061/dryad.pq0cs6h/4
title: acquiring_the_text_collections

description: Instructions for where to find the TUH EEG corpus.
DOI: 10.5061/dryad.r5t8d04/1
title: all_eqtl_w_ase.txt
DOI: 10.5061/dryad.r5t8d04/2
title: All eQTLs using total expression only

description: all tested SNP-gene pairs using total expression model (suez) only. p_geno is the p-value for a marginal effect eQTL, p_interact for a response-eQTL.
DOI: 10.5061/dryad.tj48997/1
title: 50_percent_taxon_coverage

description: 50% taxon coverage concatenated matrix used in phylogenomic analyses (phylip format).
DOI: 10.5061/dryad.tj48997/2
title: 70_percent_taxon_coverage

description: 70% taxon coverage concatenated matrix used in phylogenomic analyses (phylip format).
DOI: 10.5061/dryad.tj48997/3
title: Individual_loci_pre_manual_editing

description: Zip archive containing multiple sequence alignments for all loci produced from phyluce analyses, before manual editing of individual loci.
DOI: 10.5061/dryad.tj48997/4
title: Individual_loci_post_manual_editing

description: Zip archive containing multiple sequence alignments for all loci produced from phyluce analyses, after manual editing of individual loci.
DOI: 10.5061/dryad.tj48997/5
title: Raw_assemblies

description: Zip archive containing raw contig assemblies (fasta format) for all samples used in this study.
DOI: 10.5061/dryad.068d0d0/11
title: alphaproteobacteria_mitochondria_untreated.aln

description: Concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/12
title: alphaproteobacteria_mitochondria_stationarytrimmed.aln

description: Stationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/13
title: alphaproteobacteria_mitochondria_SR4recoded.aln

description: SR4 recoded, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/14
title: alphamito38.concat.untreated.aln

description: Concatenated supermatrix alignment of 38 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/15
title: alphamito38.concat.stattrim.aln

description: Stationary-trimmed, concatenated supermatrix alignment of 38 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/16
title: nuclearEncoded29_concat_Composite.untreated.aln

description: Concatenated supermatrix alignment of 29 genes conserved among alphaproteobacteria and mitochondrial genes encoded on nuclear eukaryotic genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/17
title: nuclearEncoded29_concat_Composite.stattrim.aln

description: Stationary-trimmed, concatenated supermatrix alignment of 29 genes conserved among alphaproteobacteria and mitochondrial genes encoded on nuclear eukaryotic genomes. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/18
title: alphamito24.otherMitoTaxa.concat.untreated.aln

description: Concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, a more diverse set of mitochondria has been selected. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/9
title: alphaproteobacteria_stationarytrimmed.aln

description: Stationary trimmed, concatenated supermatrix alignment of 72 genes conserved among alphaproteobacteria. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.1224pr2/1
title: Hembry_et_al_specimen_locality_data

description: Specimen locality and host plant data for moths in the genus Epicephala (Lepidoptera: Gracillariidae; leafflower moths) collected for this study in the Society Islands, French Polynesia during the period 2007-2011. Specific locality data withheld to protect rare native plant species. Identical to Table S2 for Supplementary Information for the journal article.
DOI: 10.5061/dryad.1224pr2/2
title: DNA sequence data from Society Islands Epicephala spp.

description: Novel DNA sequence data generated for this study from undescribed species in the genus Epicephala (Insecta: Lepidoptera: Gracillariidae). These data represent three loci: mitochondrial COI, and nuclear EF1-α and ArgK. Sequences have also been uploaded to GenBank, but are being processed at time of submission, so GenBank numbers are not included in this file; for GenBank numbers, please see main text of published manuscript. Sequences may also be matched using collection numbers (nine-character alphanumeric codes beginning with dhh; these codes also are used in the specimen locality data file in this Dryad package, David Hembry's original field notes, and corresponding GenBank submissions).
DOI: 10.5061/dryad.1224pr2/3
title: Hembry_et_al_Epicephala_tree.txt

description: Phylogenetic hypothesis for Society Islands Epicephala, recovered using Bayesian inference implemented in MrBayes. Tip labels represent specimen numbers and host species (in the clade Glochidion in the genus Phyllanthus s. l.) from which specimens were reared, and are from the present study as well as Hembry et al. (2013) Proc. Roy. Soc. B. Many tip labels follow the Supplementary Appendix in Hembry et al. (2013) Proc. R. Soc. B. This tree corresponds to Figure 1 in the present manuscript.
DOI: 10.5061/dryad.1224pr2/4
title: Hembry_networks_metadata

description: Metadata for the seven networks files (Hembry_et_al_Amami_quantitative.xlsx, Hembry_et_al_Huahine_quantitative.xlsx, Hembry_et_al_Iriomote_quantitative.xlsx, Hembry_et_al_Ishigaki_quantitative.xlsx, Hembry_et_al_Moorea_quantitative.xlsx, Hembry_et_al_Okinawa_quantitative.xlsx, Hembry_et_al_Tahiti_quantitative.xlsx) included in the present submission. Identical to metadata which will be uploaded to the Interaction Web DataBase (https://www.nceas.ucsb.edu/interactionweb/) and mangal (mangal.io).
DOI: 10.5061/dryad.1224pr2/5
title: Glochidion-Epicephala_network_Amami

description: See Hembry_networks_metadata for description. Data originally from Kawakita and Kato (2006) Mol. Ecol.
DOI: 10.5061/dryad.1224pr2/6
title: Glochidion-Epicephala_network_Huahine

description: See Hembry_networks_metadata for description. Data novel to this study.
DOI: 10.5061/dryad.5f24ks4/4
title: 16S raw otu table and taxonomy table

description: This biom file contains the unrarefied otu table and taxonomy table of 16S reads. The matching sample data file is "raw16S_sampledata.csv". The READ ME file for the RData image contains all the explanations of the data files.
DOI: 10.5061/dryad.5f24ks4/5
title: raw16S_sample_data

description: This sample data corresponds to the raw 16S biom file. The data is described in the RData READ ME file.
DOI: 10.5061/dryad.5f24ks4/6
title: rawITS_otus_tax

description: This biom file contains the unrarefied ITS otu table, taxonomy file, and FUNguild annotations. The corresponding sample data is "rawITS_sample_data.csv".
DOI: 10.5061/dryad.5f24ks4/7
title: rawITS_sample_data

description: This ITS sample data file matches the unrarefied ITS biom data. The READ ME file for the RData contains all the sample data descriptions.
DOI: 10.5061/dryad.62g52g4/1
title: Trait and fitness measurements of Oxalis montana in transplant experiment; Plastic and genetic drivers of community turnover

description: Measurements of height, leaf area, specific leaf area (SLA) on individuals of Oxalis montana from a reciprocal transplant experiment along an elevational gradient. Assessments of individual survival after first winter in the field and assessment of final survival at the end of the growing season. Measurements of total dry biomass after growing season and biomass covariate variable used as a proxy of initial biomass. Sites and transects of origin and of transplant are indicated for each individual, as well as transplant block within transplant site. See manuscript for methodological details on measurements.
DOI: 10.5061/dryad.689hp02/1
title: data_JEcol-0797

description: Data were collected in 2008 & 2014 in a field manipulation experiment conducted in a temperate steppe in northern China. Abbreviated headlines are as follows: "ANPP" = aboveground plant community productivity; "N" = nitrogen; "W" = water; "NRI" = the net relatedness index; “CWM” = community weighted mean; “S” = plant stature; “LA” = leaf area, “SLA” = specific leaf area; “LDMC” = leaf dry matter content; “LN” = leaf nitrogen concentration; FDis = functional dispersion; "SW" = soil water content; "IN" = soil inorganic nitrogen.
DOI: 10.5061/dryad.6pq3250/1
title: all traits averages

description: species-level averages for 15 species of cardamine growing in the Alps.
DOI: 10.5061/dryad.7cp50/3
title: SleepEcology_MappingFile

description: Data mapping file.
DOI: 10.5061/dryad.8dt0gd1/1
title: Silene_Trait

description: The sheet named "data Liu & Karrenberg" contains  data of phenotype measurements. The second sheet named "Column_explanation" contains explanation for each column in the first sheet.
DOI: 10.5061/dryad.8pt77k0/1
title: Baseline characteristics of participants

description: Data for HIV-negative participants who have culture-proven drug-susceptible tuberculosis and a baseline CT scan.
DOI: 10.5061/dryad.8pt77k0/2
title: Longitudinal cough and sputum results

description: Daily cough and sputum results for each participant during treatment.
DOI: 10.5061/dryad.8t8v6/1
title: MIP testing and absolute density testing

description: Raw data for MIP testing and absolute density testing
DOI: 10.5061/dryad.8t8v6/2
title: 1000xRED autofluorescence Z-stack

description: The .CZI files can be opened by Zen software. http.www.zeiss.com/microscopy/us/products/microscopesoftware/zen/czi.html.
DOI: 10.5061/dryad.dp8b07r/15
title: Sub15
DOI: 10.5061/dryad.dp8b07r/16
title: Sub16
DOI: 10.5061/dryad.dp8b07r/17
title: Sub17
DOI: 10.5061/dryad.dp8b07r/18
title: Sub18
DOI: 10.5061/dryad.dp8b07r/19
title: Sub19
DOI: 10.5061/dryad.dp8b07r/20
title: Sub20
DOI: 10.5061/dryad.dp8b07r/21
title: Sub21
DOI: 10.5061/dryad.f6q5j/1
title: Labelling and biomass data

description: Labelling data (first sheet) - molar stable isotope ratio of nitrogen and carbon in plant samples, C and N molar concentration, dry biomass and calculations of amounts of 13C and 15N originating form pulse-labelling. Data includes only integrated ramet pairs. Biomass data (second sheet) - dry biomass of plant samples. Includes both integrated and severed ramet pairs. Description of column names is provided in the file.
DOI: 10.5061/dryad.f8h7h/1
title: Candela et al. Supplemental Data 1

description: Supplemental Data 1.- List of cavioid specimens examined.
DOI: 10.5061/dryad.f8h7h/2
title: Candela et al. Supplemental Data 2

description: Characters and character states definitions
DOI: 10.5061/dryad.f8h7h/3
title: Candela et al. Supplemental Data 3

description: Data matrix
DOI: 10.5061/dryad.r20d2s4/1
title: Raw data from Paleobiology Database

description: These are the raw data prior to any cleaning to be used with LatDevRcode.R, Palaeo222cells.csv, stages_2012PBDB.csv and TimeSeriesUsed.csv
DOI: 10.5061/dryad.r20d2s4/2
title: R code for data cleaning and analyses

description: This contains the steps to obtain basic latitudinal deviations i.e. to build Figure 3 from the paper.
DOI: 10.5061/dryad.r20d2s4/3
title: Equal area geographical cells

description: These contain the details of the geographical cells used, obtained using R package 'icosa'.
DOI: 10.5061/dryad.r20d2s4/4
title: Time bins appropriate for the data
DOI: 10.5061/dryad.r20d2s4/5
title: Prepared latitudinal deviation time series

description: Contains the pre-prepared time series of latitudinal deviations for the Northern and Southern Hemispheres and using hemisphere switching. These are binned to stages. Also included are the binned temperature data from Veizer & Prokoph, 2015.
DOI: 10.5061/dryad.r5t8d04/10
title: rarg_trans_eqtl.txt

description: trans eQTL for the rs2229774 non-synonymous variant in RARG. p_geno: marginal effect eQTL p-value. p_interact: response eQTL p-value. Columns starting "q_" correspond to Benjamini-Hochberg adjusted p-values.
DOI: 10.5061/dryad.r5t8d04/11
title: sample_table

description: he rows of this table correspond to the columns of log2_counts_per_million.txt.gz
DOI: 10.5061/dryad.r5t8d04/3
title: all_splicing_qtl.txt

description: all tested SNP-intron pairs. Columns are analogous to all_eqtl.txt.gz.
DOI: 10.5061/dryad.r5t8d04/4
title: Sample meta data

description: meta data associated with each sample, and columns:
	*  **id** - unique ID for sample. Composed of sample number, cell line, and dosage information.
	*  **sample** - sample number. Range from 1-230. Each set of 5 are the treatments for one individual, in increasing concentrations of dox.
	*  **cell_line** - the cell line number. Each cell line corresponds one individual.
	*  **dbgap** - anonymized ID for matching cell_line to genotypes.
	* **sample_id** - anonymized ID assigned to each unique combination of `dbgap` and `dosage.
	*  **dosage** - the concentration of dox used in the treatment.
	*  **rin** - the RNA Integrity Number (RIN). Range from 1-10.
	*  **rna_conc** - the RNA concentration (ng/uL) after RNA extraction.
	*  **lib_prep_batch** - the batches the libraries were prepared in.
	*  **index** - the TruSeq adapter index used for multiplexing.
	*  **library_conc** - the concentration (ng/uL) of the library measured on the Bioanalyzer.
	*  **fragment_size** - the mean fragment size as measured on the Bioanalyzer.
	*  **qpcr** - the library concentration (nmol) as measured via qPCR.
	*  **qpcr_dilute** - the concentration (nmol) of the diluted library.
	*  **master_mix** - the master mix for pooling libraries. 10 samples (2 individuals) per master mix.
	*  **lane_perc** - The percentage of sequences in one lane that were assigned to a sample.
DOI: 10.5061/dryad.r5t8d04/5
title: embryoid_staining

description: iPSC quality control. This represents a superset of the lines differentiated into cardiomyocytes.
DOI: 10.5061/dryad.r5t8d04/6
title: leafcutter_counts.txt

description: LeafCutter alternative splicing quantification on all samples.
DOI: 10.5061/dryad.r5t8d04/7
title: leafcutter_samples

description: the rows of this table correspond to the columns of leafcutter_counts.txt.gz
DOI: 10.5061/dryad.r5t8d04/8
title: log2_counts_per_million.txt

description: gene expression quantification for 217 samples with &gt;10M exonic reads in our dataset.
DOI: 10.5061/dryad.r5t8d04/9
title: purity

description: FACS measurements of cardiomyocyte purity, columns are: 
	* cell_line - the cell line number. Each cell line corresponds one individual.
	* dbgap - anonymized ID for matching cell_line to genotypes.
	* flow_date - date of flow cytometry experiment
	* purity - percentage of cells that expressed cardiac troponin (cTnI and cTnT)
DOI: 10.17632/rd4kyr4fym.1
title: Data for: How Do We Diagnose and Treat Epilepsy with Myoclonic-Atonic Seizures (Doose Syndrome)? Results of the Pediatric Epilepsy Research Consortium Survey

description: Survey and results raw data of the survey sent to neurologists in PERC, AES, CNS to determine how Epilepsy with Myoclonic Atonic Seizures (EMAS, Doose) is evaluated and treated.
DOI: 10.5061/dryad.068d0d0/19
title: alphamito24.otherMitoTaxa.concat.stattrim.aln

description: Stationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, a more diverse set of mitochondria has been selected. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/20
title: alphamito24.concat.NoOutgroups.untreated.aln

description: Concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, the outgroups MarineProteo1, Magnetococcales, Beta- and Gammaproteobacteria have been removed. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.068d0d0/21
title: alphamito24.concat.NoOutgroups.stattrim.aln

description: Stationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, the outgroups MarineProteo1, Magnetococcales, Beta- and Gammaproteobacteria have been removed. See associated publication for technical details on how this alignment was prepared.
DOI: 10.5061/dryad.1224pr2/10
title: Glochidion-Epicephala_network_Okinawa

description: See Hembry_networks_metadata for description. Data originally from Kawakita and Kato (2006) Mol. Ecol.
DOI: 10.5061/dryad.1224pr2/11
title: Glochidion-Epicephala_network_Tahiti

description: See Hembry_networks_metadata for description. Data novel to this study.
DOI: 10.5061/dryad.1224pr2/7
title: Glochidion-Epicephala_network_Iriomote

description: See Hembry_networks_metadata for description. Data originally from Kawakita and Kato (2006) Mol. Ecol.
DOI: 10.5061/dryad.1224pr2/8
title: Glochidion-Epicephala_network_Ishigaki

description: See Hembry_networks_metadata for description. Data originally from Kawakita and Kato (2006) Mol. Ecol.
DOI: 10.5061/dryad.1224pr2/9
title: Glochidion-Epicephala_network_Moorea

description: See Hembry_networks_metadata for description. Data novel to this study.
DOI: 10.5061/dryad.14n6t17/1
title: Statistics for MS

description: Complete stat for MS
DOI: 10.5061/dryad.2dh0223/1
title: DataS1

description: The archive has 2 files. The first file has general information about captured animals (estimated age, weight, collar used, etc.). The second file has general information on animals' location.
DOI: 10.5061/dryad.4h44313/1
title: Pratylenchus penetrans_predicted CDS

description: Pratylenchus penetrans predicted CDS.
DOI: 10.5061/dryad.4h44313/2
title: Pratylenchus penetrans_predicted protein

description: Pratylenchus penetrans predicted protein sequences
DOI: 10.5061/dryad.5vm48h0/1
title: Data_Mueller_et_al._2018

description: This Zip archive includes two csv-files. These files provide all data used for the analyses included in the research article.
DOI: 10.5061/dryad.61m318c/1
title: Phenology data

description: This file contains fruiting phenology data, from 2005-2016, for 457 individuals from 69 common tree species in Ranomafana National Park, Madagascar.
DOI: 10.5061/dryad.61m318c/2
title: Rainfall data

description: This file contains monthly rainfall data for Ranomafana National Park, collected from 2005-2016 from the Centre ValBio research station.
DOI: 10.5061/dryad.7cp50/1
title: SleepEcology_OTU_rar_V2

description: Rarefied dataset used in analyses. Sequences were rarefied to 5600 reads per sample.
DOI: 10.5061/dryad.7cp50/2
title: SleepEcology_Code

description: Workflow used to process raw data files in the UPARSE pipeline and analyze sequencing output within the R environment.
DOI: 10.5061/dryad.7cp50/4
title: SleepEcology_seqs.fastq

description: Raw data file. Microbes were collected in relation to 41 chimpanzee beds located in the Issa Valley, western Tanzania, between August 2013 and April 2014. All samples were collected with dual-tipped sterile BBL Culture Swabs, and DNA was subsequently extracted with a MO BIO PowerSoil DNA Isolation Kit. Extracted DNA was sequenced on the Illumina MiSeq platform, targeting the V1-V2 region of the 16S rRNA gene.
DOI: 10.5061/dryad.7m2q041/1
title: Table

description: Table
DOI: 10.5061/dryad.9mv6d51/1
title: Unmasked single-gene alignments

description: Compressed file containing unmasked single-gene alignments used to generate the concatened phylogenomic datasets
DOI: 10.5061/dryad.9mv6d51/2
title: Concatenated datasets used for phylogenomic analysis

description: Compressed file containing the two masked concatenated datasets used in the full phylogenomic analyses
DOI: 10.5061/dryad.cv1f50m/1
title: Data_archive

description: This compressed archive includes multiple other files including data files (in .csv format for tabular data, .Rdata files for data from higher dimensional arrays, and .tif files for landscape grids) and R scripts for running invasion simulations and to read and evaluate data files. Specific descriptions of each file are supplied in the ReadMe.txt file.