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1,773 results for “Supplementary data,”
Chapter 3 supplementary data
<p>this is a test</p>
Supplementary data: Single Cardiac Ventricular Myosins are Autonomous Motors
<p>The files in this record contain partial data for the paper ‘Single Cardiac Ventricular Myosins are Autonomous Motors’. It includes one movie for unloaded Qdot data of WT, A57G and E143K, one movie for data at 3ug/ml of alpha-actinin, and related files.</p>
Supplementary data for the manuscript, "Comprehensive Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Repertoires"
<p>This repository contains data and code used in the manuscript "Comparative Assessment of Physiochemical Metrics for the Clustering of Adaptive Immune Receptor Repertoires" by Girgis et al. For additional information regarding how these data were used, please refer to our manuscript.</p> <p>Code is organized per figure in the main text. Each figure folder contains a 'script-inputs' folder and 'script-outputs' folder. The outputs folder is empty and may be populated with graphs and results tables by executing code within the directory. The inputs folder contains some pre-formatted data which may be used in executing code. Most of these inputs may be generated from scratch using raw data (ie the results of Homolig clustering on simulated repertoires) but may require substantial time and/or computational resources. Raw patient data used in Figure 6 (Pancreatic cancer anti-mKRAS TCRB repertoire clustering) and Figure 7 (Rheumatoid arthritis TCRB and IGH repertoires) are not included here. However, several graphs may be reproduced stripped of sequence-specific data. Pancreatic cancer patient repertoire data will be made available on dbGaP,study accession number phs003425.v1.p1. Rheumatoid arthritis patient data will be made available on ImmuneAccess, accession pending.</p> <p>To browse repo, first unzip all subdirectories: </p> <blockquote> <p><code>for f in *.zip; do</code><br><code> unzip "$f"</code><br><code>done</code></p> </blockquote> <p>All non-code files have been compressed to .gz format. To decompress, use: <code>gzip -dr *</code>, or <code>pigz -dr ./raw-data/* </code>for parallel decompression (recommended). </p> <p>Alexander Girgis <br>agirgis3@jhmi.edu <br>July 2025 </p>
Supplementary Material for the paper entitled "Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data"
<p>This repo contain supplementary tables from the manuscript entitled: "Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data". Clustering is a common way to identify cell types in single-cell RNA-sequencing (scRNA-seq) data. Unfortunately, current methods (i) require users to make human-in-the-loop decisions, which adds significant runtime to bioinformatic analyses, and (ii) reuse the same data twice when testing for differentially expressed genes, which can lead to an increased number of false discoveries. In this work, we overcome these limitations with NCLUSION: a Bayesian nonparametric method that simultaneously clusters cells and selects marker genes. NCLUSION operates without user-defined heuristics to set model parameters and leverages variational expectation-maximization (EM) for posterior inference which allows it to scale well up to 1 million cells. By analyzing publicly available datasets, we illustrate that NCLUSION matches the state-of-the-art clustering performance of competing approaches, achieves improved computational efficiency, and directly enables identification of biologically relevant gene sets driving cluster definitions.</p>
Supplementary Data and Scripts for 'Extreme heat and drought typical of an end-of-century climate could occur soon and repeatedly over Europe', Suarez-Gutierrez et al., 2023
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Supplementary material 2 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Detailed procedure for macroinvertebrate bio-area measurements
Supplementary material 3 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Supplementary results
Supplementary material 1 from: Schneider AS, Knüsel M, Altermatt F (2023) Assessment of occurrence, diversity, and biomass of macroinvertebrates in Swiss groundwater systems using citizen science data. Subterranean Biology 46: 147-164. https://doi.org/10.3897/subtbiol.46.112569
Bio-area and biomass relationship
Supplementary Materials of the Manuscript: "Evolving a Methodology for Assessing Pesticide Pressure on Water Bodies under Data Scarce Conditions in compliance with the European Green Deal – Case Study on Marmara Basin in Türkiye-ID:sustainability-2755948"
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Supplementary material 2 from: Jasso-Martínez JM, Brady SG, Kula RR (2023) Phylogenetic affinities of the non-cyclostome subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) confirmed by ultraconserved element data. Journal of Hymenoptera Research 96: 1017-1030. https://doi.org/10.3897/jhr.96.111012
Maximum likelihood tree resulting from the 25% complete matrix
Supplementary material 3 from: Luo T, Mao M-L, Lan C-T, Song L-X, Zhao X-R, Yu J, Wang X-L, Xiao N, Zhou J-J, Zhou J (2023) Four new hypogean species of the genus Triplophysa (Osteichthyes, Cypriniformes, Nemacheilidae) from Guizhou Province, Southwest China, based on molecular and morphological data. ZooKeys 1185: 43-81. https://doi.org/10.3897/zookeys.1185.105499
Morphological characters and measurement data
Supplementary material 2 from: Luo T, Mao M-L, Lan C-T, Song L-X, Zhao X-R, Yu J, Wang X-L, Xiao N, Zhou J-J, Zhou J (2023) Four new hypogean species of the genus Triplophysa (Osteichthyes, Cypriniformes, Nemacheilidae) from Guizhou Province, Southwest China, based on molecular and morphological data. ZooKeys 1185: 43-81. https://doi.org/10.3897/zookeys.1185.105499
GPS information on the geographical distribution of 39 hypogean species of the genus Triplophysa
Supplementary Materials for article entitled 'On Italian Spatial Prepositions and Measure Phrases: Reconciling Data with Theoretical Accounts', published in Linguistics
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FIGURE 49 in Supplementary data and taxonomic changes in the subterranean beetles of the Balkan Peninsula from July 1 2016 to September 30 2023
FIGURE 49. Speoplanes biocovensis Müller, 1934, 7.50–9.00 mm (original).
FIGURE 28. Anthroherpon spelaebatoides Noesske, 1914 in Supplementary data and taxonomic changes in the subterranean beetles of the Balkan Peninsula from July 1 2016 to September 30 2023
FIGURE 28. Anthroherpon spelaebatoides Noesske, 1914 (ex Hlaváč et al. 2017: 89), 3.90–4.00 mm.
Supplementary Dataset_Spreadsheets and data sources
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METEOROLOGICAL AND AGRICULTURAL DROUGHT RISK ASSESSMENT VIA KAPLAN-MEIER SURVIVABILITY ESTIMATOR SUPPLEMENTARY DATA
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Supplementary material 1 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Table S1
Supplementary material 2 from: Magesh S, Jonsson V, Bengtsson-Palme J (2019) Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. Metabarcoding and Metagenomics 3: e36236. https://doi.org/10.3897/mbmg.3.36236
Figure S1
Supplementary material 2 from: Reid BN, Servis JA, Timmers M, Rohwer F, Naro-Maciel E (2022) 18S rDNA amplicon sequence data (V1–V3) of the Palmyra Atoll National Wildlife Refuge, Central Pacific. Metabarcoding and Metagenomics 6: e78762. https://doi.org/10.3897/mbmg.6.78762
Figure S2
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.