cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25024466
title: Processed clonal barcoding samples from both gDNA and 10X cDNA associated with scRNAseq experiment

description: Processed barcoding reads that have been processed using code: https://github.com/SydShafferLab/BarcodeAnalysis. Raw data is found in other folders in this project ("Demultiplexed sequencing reads of barcodes from 10x cDNA associated with scRNAseq experiment" and "Demultiplexed sequencing reads of barcodes from gDNA associated with scRNAseq experiment - split across 3 sequencing runs"). Starcode_outputs are counts per barcode for each condition (from gDNA or 10X cDNA). FASTQ are processed fastqs of the barcodes from 10X cDNA for input into CellRanger. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.6084/m9.figshare.25021745
title: Demultiplexed sequencing reads of barcodes from 10x cDNA associated with scRNAseq experiment

description: Sequenced clonal barcoding reads associated with 10X barcodes. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.6084/m9.figshare.25021745.v1
title: Demultiplexed sequencing reads of barcodes from 10x cDNA associated with scRNAseq experiment

description: Sequenced clonal barcoding reads associated with 10X barcodes. Associated manuscript: https://www.biorxiv.org/content/10.1101/2023.03.24.534152v1.full
DOI: 10.6084/m9.figshare.24975744.v3
title: Estimating Ephemeral Streams QGIS Layer Packages, Map Files, and Methods

description: This dataset was used to estimate total ephemeral stream length within the Coeur d'Alene, Fort Apache, and Menominee Reservations. It includes data that is publicly available through the USGS "The National Map" (USGS TNM Download v2.0), including NHDPlus High Resolution hydrography data, and Contour (1:24,000-scale) elevation data. It also includes geographic boundaries for the above mentioned Native American Reservations, as well as "eph5ha" raster data, developed by Kurt A. Fesenmyer, which was used to approximate ephemeral stream locations. The remaining layers in the dataset include exported, site-specific NHDPlus hydrography data, and hand-digitized, estimated ephemeral streams, based on the eph5ha raster data. A map PNG of all three reservations is also included, as well as the map file used to create that map image. Lastly, a PDF of the methods used for this mapping project is also attached.
DOI: 10.5281/zenodo.10535682
title: Data used in the paper "On the Usefulness of Python Structural Pattern Matching: An Empirical Study"

description: Structure

In the `answers` folder, you can find the responses given by the participants. Each file contains JSON objects (one answer-one line) with the participants' answer to a given example.

The code snippets shown to the participants are located in the `user_study_files` folder. The `mapping.txt` file contains the mapping between the identifiers and the files. The `old` folder contains the code snippets before transformation, while the `new` folder contains the transformed snippets.
DOI: 10.5281/zenodo.10535683
title: Data used in the paper "On the Usefulness of Python Structural Pattern Matching: An Empirical Study"

description: Structure

In the `answers` folder, you can find the responses given by the participants. Each file contains JSON objects (one answer-one line) with the participants' answer to a given example.

The code snippets shown to the participants are located in the `user_study_files` folder. The `mapping.txt` file contains the mapping between the identifiers and the files. The `old` folder contains the code snippets before transformation, while the `new` folder contains the transformed snippets.
DOI: 10.6084/m9.figshare.24975744
title: Estimating Ephemeral Streams QGIS Layer Packages, Map Files, and Methods

description: This dataset was used to estimate total ephemeral stream length within the Coeur d'Alene, Fort Apache, and Menominee Reservations. It includes data that is publicly available through the USGS "The National Map" (USGS TNM Download v2.0), including NHDPlus High Resolution hydrography data, and Contour (1:24,000-scale) elevation data. It also includes geographic boundaries for the above mentioned Native American Reservations, as well as "eph5ha" raster data (Fesenmyer et al. 2021), which was used to approximate ephemeral stream locations. The remaining layers in the dataset include exported, site-specific NHDPlus hydrography data, and hand-digitized, estimated ephemeral streams, based on the eph5ha raster data. A map PNG of all three reservations is also included, as well as the map file used to create that map image. Lastly, a PDF of the methods used for this mapping project is also attached.
DOI: 10.6084/m9.figshare.24975744.v5
title: Estimating Ephemeral Streams QGIS Layer Packages, Map Files, and Methods

description: This dataset was used to estimate total ephemeral stream length within the Coeur d'Alene, Fort Apache, and Menominee Reservations. It includes data that is publicly available through the USGS "The National Map" (USGS TNM Download v2.0), including NHDPlus High Resolution hydrography data, and Contour (1:24,000-scale) elevation data. It also includes geographic boundaries for the above mentioned Native American Reservations, as well as "eph5ha" raster data (Fesenmyer et al. 2021), which was used to approximate ephemeral stream locations. The remaining layers in the dataset include exported, site-specific NHDPlus hydrography data, and hand-digitized, estimated ephemeral streams, based on the eph5ha raster data. A map PNG of all three reservations is also included, as well as the map file used to create that map image. Lastly, a PDF of the methods used for this mapping project is also attached.
DOI: 10.6084/m9.figshare.24975744.v4
title: Estimating Ephemeral Streams QGIS Layer Packages, Map Files, and Methods

description: This dataset was used to estimate total ephemeral stream length within the Coeur d'Alene, Fort Apache, and Menominee Reservations. It includes data that is publicly available through the USGS "The National Map" (USGS TNM Download v2.0), including NHDPlus High Resolution hydrography data, and Contour (1:24,000-scale) elevation data. It also includes geographic boundaries for the above mentioned Native American Reservations, as well as "eph5ha" raster data (Fesenmyer et al. 2021), which was used to approximate ephemeral stream locations. The remaining layers in the dataset include exported, site-specific NHDPlus hydrography data, and hand-digitized, estimated ephemeral streams, based on the eph5ha raster data. A map PNG of all three reservations is also included, as well as the map file used to create that map image. Lastly, a PDF of the methods used for this mapping project is also attached.
DOI: 10.5061/dryad.j21n1/1
title: Seedling demography for African mahogany in Benin

description: These data show the basal diameter (cm), heights (m) measured on individual seedlings and saplings of Khaya senegalensis (Meliaceae) yearly from 2004 to 2007. From 2005-2007, we report if individual survived or not and the previously measured basal diameter and height (if applicable). Individuals have unique (aluminum) tag number within population. A total of 12 populations were monitored for 4 years and these populations were selected randomly in two ecological regions (wet or dry) and in each region populations were equally divided between high and low foliage and bark harvesting intensities.
DOI: 10.5061/dryad.j21n1/2
title: Seedling microhabitat for African mahogany in Benin

description: We collected four years (2004-2007) seedling and sapling microhabitat and abundance data within ten 10 x 10m plot within each of 12 population of Khaya senegalensis in Benin, West Africa. Within each plot, we collected data yearly on grass cover (%), percent plot burned, and percent cover of non-graminaceous understory species (2005-2007), and tree canopy cover (2006-2007). We also counted seedling (&lt;2 cm) and sapling number in each plot from 2004-2006. These microhabitats data are for the same individuals as in Data 1 file (Khaya_Seedling_Demography.csv).
DOI: 10.5061/dryad.r0v35/1
title: suicide attempt data_2
DOI: 10.5061/dryad.5dh5f/1
title: Phenotype and SNP Genotype Data

description: This Excel file contains information on 906 field-grown backcross1 sunflower plants.Field site is identified in column Z.Plants are identified by the number in column AA.Columns A-Y contain field-measured trait data.  Trait names correspond to the abbreviations in Table 1 of the associated manuscript.Columns AH - HO contain SNP genotype data; A = H. a. annuus allele; D = H. debilis allele.
DOI: 10.5061/dryad.5dh5f/2
title: Linkage Map

description: This Excel file contains the estimated linkage map for the H. a. annuus x H. debilis backcross1 mapping populations.The position of each marker on the linkage group is given in centiMorgans (cM).
DOI: 10.5061/dryad.6cj48/1
title: Caribou-cougar-deer data for Figure 5.

description: The first case study used to validate the ODE model.
DOI: 10.5061/dryad.6cj48/2
title: Moose-wolf-caribou data for Figure 6

description: Data for figure 6 for caribou-moose-wolf case study.
DOI: 10.5061/dryad.mv5dh/1
title: proc Bcomplete
DOI: 10.5061/dryad.dc335/1
title: Sperm competition experimental data

description: The file contains the data collected during a sperm competition experiment conducted on captive bred zebra finches. Using a mate switching experimental design, we investigated whether sperm length (either long or short) influenced the number of sperm from each competing male that reached the ovum, and the number of embryos sired by each male.
DOI: 10.5061/dryad.dc335/2
title: Summary paternity

description: The file contains the summary paternity data for each individual trio of birds (one female and one pair of males) used in the sperm competition experiment. This file was required to calculate summary statistics for the manuscript.
DOI: 10.5061/dryad.dc335/3
title: Sperm length and competitive success

description: This R script contains the code that was used to carry out the statistical tests and summary data in the manuscript and for table S5 in the electronic supplementary material
DOI: 10.5061/dryad.dc335/4
title: Sperm quality comparison sperm competiton males

description: This data file contains the results of the sperm quality analyses carried out on all male zebra finches that were used in the sperm competition experiments. Data are arranged side by side for each pair of competing males, and analysed by comparing the sperm quality long and short sperm males, using a paired design.
DOI: 10.5061/dryad.n40m6/1
title: Choice data

description: Data on dietary choice for nutrients
DOI: 10.5061/dryad.n40m6/2
title: Male fertility data

description: Data examining nutrient effects of male fertility
DOI: 10.5061/dryad.n40m6/3
title: Sperm data

description: Data examining the effects of nutrients on sperm number and sperm viability
DOI: 10.5061/dryad.2fc32/1
title: DC1

description: ITS2 rDNA sequence data partitioned into individual soil samples based on tag identifiers.
DOI: 10.5061/dryad.dc335/10
title: Relatedness scores

description: This R script contains code to calculate the mean relatedness scores between pairs of males and females, and between the pairs of competing males.
DOI: 10.5061/dryad.dc335/11
title: Relatedness scores_male x female_ male x male

description: The data file contains relatedness scores for the males and females arranged so the male x female and male x male mean scores can be calculated
DOI: 10.5061/dryad.dc335/12
title: Readme
DOI: 10.5061/dryad.dc335/5
title: Testes mass sperm competition males

description: This file contains the left testes mass data from the males used in sperm competition experiment
DOI: 10.5061/dryad.dc335/6
title: Seminal glomera mass

description: This file contains the left and right seminal glomera mass data from a small number of male zebra finches producing either long or short sperm. These males were not used in the sperm competition experiments.
DOI: 10.5061/dryad.dc335/7
title: Copulation rate

description: This file contains the data from a study investigating whether male zebra finches with different sperm lengths (long or short) copulated with females at the same rate. These males were not used in the sperm competition experiments.
DOI: 10.5061/dryad.dc335/8
title: Sperm quality comparisons

description: This R script contains the code to investigate whether sperm quality varies with sperm length (long or short), and whether left testes mass is related to sperm length. Code is also provided for additional studies investigating whether sperm length is related to seminal glomera mass and copulation rate (not that these final two studies did not use the males from the sperm competition experiments. The results of all statistical tests were used to make tables S1 - S4 in electronic supplementary material 2.
DOI: 10.5061/dryad.dc335/9
title: Relatedness scores

description: This file contains the relatedness scores for all males and females used in the sperm competition experiments. Data were obtained from the detailed zebra finch pedigree and estimated using the R package Pedantics.
DOI: 10.5061/dryad.2fc32/2
title: DC2
DOI: 10.5061/dryad.2fc32/3
title: DC3
DOI: 10.5061/dryad.2fc32/4
title: DC4
DOI: 10.5061/dryad.2fc32/5
title: DC5
DOI: 10.5061/dryad.2fc32/6
title: DT1
DOI: 10.5061/dryad.2fc32/7
title: DT2
DOI: 10.5061/dryad.2fc32/8
title: DT3
DOI: 10.5061/dryad.2fc32/9
title: DT4
DOI: 10.5061/dryad.bs332/1
title: Thomas_etal_2014_Dryad

description: Data were collected from 2008-2010 at various sites on Dominica, Lesser Antilles.  Abbreviated headlines are as follows: "year" = year of data collection; "species" = species code; "dbh" = diameter at 1.3 m in cm; "ht" = tree height in m; "rep" = reproductive status with 0 indicating no reproductive structures, and 1 indicating presence of reproductive structures; "CrClass" = crown exposure class on 1-5 scale; "lean" = stem lean in degrees from vertical; "lianascor" = liana load on 5 point scale; "dam" = presence/absence of crown damage (scored as 0/1); "dmgamt" = percent of crown damaged; "incallom" = excluded/included in allometric analyses (scored as 0/1).
DOI: 10.5061/dryad.bs332/2
title: Thomas_etal_2014_Dryad2

description: Data on tree allometry in exposed vs. shelter sites collected in the field at various sites in Dominica, Lesser Antilles in 2008-2010.  Abbreviated headlines are as follows: "expos" = classification of site exposure: "exp" = exposed, "sh" = sheltered; "sp" = species code; "diam_cm" = stem diameter in cm at 1.3 m height, "incallom" = excluded/included in allometric analyses based on assessment of crown and stem damage, scored as (0/1).
DOI: 10.5061/dryad.2fc32/10
title: DT5
DOI: 10.5061/dryad.2fc32/11
title: MC1
DOI: 10.5061/dryad.2fc32/12
title: MC2
DOI: 10.5061/dryad.2fc32/13
title: MC3
DOI: 10.5061/dryad.2fc32/14
title: MC4
DOI: 10.5061/dryad.2fc32/15
title: MC5
DOI: 10.5061/dryad.2fc32/16
title: MT1
DOI: 10.5061/dryad.2fc32/17
title: MT2
DOI: 10.5061/dryad.2fc32/18
title: MT3
DOI: 10.5061/dryad.2fc32/19
title: MT4
DOI: 10.5061/dryad.2fc32/20
title: MT5
DOI: 10.5061/dryad.bn547/1
title: 01ALB_phased_full

description: Phased sequence alignment of ALB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/3
title: 03DARC_phased_full

description: Phased sequence alignment of DARC sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.p5v8g/1
title: Hamm_Fordyce_Dryadcode

description: This file contains the R code used to analyze and visualize the data presented in our paper
DOI: 10.5061/dryad.p5v8g/2
title: Hamm_Fordyce_data_1

description: R data file containing all objects used or generated as part of this research
DOI: 10.5061/dryad.p5v8g/3
title: Hamm_Fordyce_Dryad

description: Zip file with all data in raw form.
DOI: 10.5061/dryad.v3g17/1
title: PLoS ONE data

description: Contains the raw data of the measurements and logbook. UT and UU -codes indicate the individual sample plates; they are individual samples of the bacteria culture described in the header row.
DOI: 10.5061/dryad.bn547/10
title: 10TSHB_phased_full

description: Phased sequence alignment of TSHB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/11
title: 11UCP2_phased_full

description: Phased sequence alignment of UCP2 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/2
title: 02AMOT_phased_full

description: Phased sequence alignment of AMOT sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/4
title: 04GRIA3_phased_full

description: Phased sequence alignment of GRIA3 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/5
title: 05IL1RAPL1_phased_full

description: Phased sequence alignment of IL1RAPL1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/6
title: 06OXA1L_phased_full

description: Phased sequence alignment of OXA1L sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/7
title: 07PPOX_phased_full

description: Phased sequence alignment of PPOX sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/8
title: 08PRKCI_phased_full

description: Phased sequence alignment of PRKCI sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/12
title: 12UCP4_phased_full

description: Phased sequence alignment of UCP4 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/13
title: 01ALB_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of ALB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/14
title: 02AMOT_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of AMOT sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/15
title: 03DARC_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of DARC sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/16
title: 04GRIA3_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of GRIA3 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/17
title: 06OXA1L_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of OXA1L sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/19
title: 08PRKCI_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of PRKCI sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/9
title: 09SPTBN1_phased_full

description: Phased sequence alignment of SPTBN1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01).
DOI: 10.5061/dryad.bn547/18
title: 07PPOX_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of PPOX sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/20
title: 09SPTBN1_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of SPTBN1 sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.bn547/21
title: 10TSHB_phased_recomb_free

description: Phased sequence alignment of the largest non-recombining blocks of TSHB sequences (phase reconstruction for the Ochotona sequences was performed using PHASE v2.1 as implemented in DnaSP v5.10.01; largest non-recombining blocks determined using IMgc).
DOI: 10.5061/dryad.k3b7d/1
title: SW Supp info dataset

description: Input file and legend
DOI: 10.5061/dryad.k3b7d/3
title: False allele SAS code

description: SAS code for calculating false alleles
DOI: 10.5061/dryad.k3b7d/4
title: Allelic dropout SAS code

description: SAS code for calculating Allelic dropout
DOI: 10.5061/dryad.s16s3/1
title: Experiment_1_Data

description: Data from Experiment 1 - Preference functions measured for varied onset accentuation. Corresponds to figure 2
DOI: 10.5061/dryad.s16s3/2
title: Experiment_2_Data

description: Raw data from Experiment 2 - Preference functions measured for varied pause durations. Corresponds to Figure 3 in text.
DOI: 10.5061/dryad.s16s3/3
title: Experiment_3_Data

description: Data from Experiment 3 - preference functions measured for varied offset amplitudes. Corresponds to Figure 4 in text.
DOI: 10.5061/dryad.s16s3/4
title: Experiment_4_Data

description: Data from Experiment 4 - preference functions measured for varied gap durations. Corresponds to Figure 5 in text.