Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
17
datasets available to search
ShareScore release 0.9.0
Dataset results
17 results for “Reading Comprehension”
QAngaroo (MedHop + WikiHop) - Constructing Datasets for Multi-hop Reading Comprehension Across Documents
<p>Most Reading Comprehension methods limit themselves to queries which can be answered using a single sentence, paragraph, or document. Enabling models to combine disjoint pieces of textual evidence would extend the scope of machine comprehension methods, but currently no resources exist to train and test this capability. We propose a novel task to encourage the development of models for text understanding across multiple documents and to investigate the limits of existing methods. In our task, a model learns to seek and combine evidence — effectively performing multihop, alias multi-step, inference. We devise a methodology to produce datasets for this task, given a collection of query-answer pairs and thematically linked documents. Two datasets from different domains are induced, and we identify potential pitfalls and devise circumvention strategies. We evaluate two previously proposed competitive models and find that one can integrate information across documents. However, both models struggle to select relevant information; and providing documents guaranteed to be relevant greatly improves their performance. While the models outperform several strong baselines, their best accuracy reaches 54.5% on an annotated test set, compared to human performance at 85.0%, leaving ample room for improvement.</p>
Comprehensive identification of pathogenic variants in retinoblastoma by long- and short-read sequencing
<p>Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal variants in RB are mostly characterized by previously used short-read sequencing (SRS) analysis, which has technical limitations in identifying structural variants (SVs) and phasing information. Long-read sequencing (LRS) technology has significant advantages over SRS in detecting SVs, phased genetic variants, and methylation. In this study, we comprehensively characterized the genetic landscape of RB using combinatorial LRS and SRS of 16 RB tumors and 16 matched blood samples. We detected a total of 232 somatic SVs, with an average of 14.5 SVs per sample across the cohort. We identified 20 distinct pathogenic variants, including <span>three</span> novel small variants and <span>five</span> <span>somatic</span> SVs. Furthermore, our analysis shows that the vast majority (93.8%) of <em>RB1</em>-disrupted patients fit the two-hit hypothesis through diverse types, including the biallelic hypermethylated promoter as well as small and large compound heterozygous mutations which were missing in SRS analysis. By constructing the evolutionary history of all genetic variants, we reveal the evolution trends that <em>RB1</em> disruption early and followed by copy number changes, including amplifications of Chr2p, and deletions of Chr16q, during RB tumorigenesis. Altogether, we characterize the comprehensive genetic landscape of RB, providing novel insights into the genetic alterations and mechanisms contributing to RB initiation and development. Our work also establishes a framework to analyze genomic landscape of cancers based on LRS data. <br><br>We took IGV screenshots of SV and SNV/indels. The IGV naming conventions for SV is: sample name, chromosome 1, start, chromosome 2, end, SV type, SV length, SV breakpoint. The IGV naming convention for SNV/indels is: sample name, chromosome, position, reference allele, alternate allele.</p>
TIdeS: a comprehensive framework for accurate open reading frame identification and classification in eukaryotic transcriptomes
<p>Includes:</p> <ul> <li>ORF predictions for 28 diverse eukaryotic taxa, employing common tools/approaches</li> <li>Raw transcriptome assemblies used for ORF predictions</li> <li>Phylogenetic trees used as the basis for contamination identification, as well as validating TIdeS's efficacy</li> <li>Various TIdeS outputs (ORF prediction/classification)</li> <li>Copy of current TIdeS source code</li> </ul>
Comprehensive Structural Variant Benchmark Dataset: 1100 VCF files from long-read sequencing of 10 NCBI individuals
<p>We initially collected 10 NCBI individuals: HG002 family pedigree data (HG002 [son], HG003 [father], HG004 [mother]), the HG005 family pedigree data (HG005 [son], HG006 [father], HG007 [mother]), the NA12878 subject, the HG00096 subject, the HG00512 subject and the CHM13 subject. Then we used PacBio (CLR: Continuous Long Read, CCS: Circular Consensus Sequencing) and Nanopore (ONT) platforms, 5 aligners and 10 callers to construct the pipelines, with most parameters set to default values. After that, except for 6 invalid pipelines(pbmm2-Nanovar, lra-Picky, lra-delly, lra-NanoVar, lra-NanoSV, lra-pbsv), we obtain 1100 VCF files.</p>
The data used in correspondence on the article entitled "Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'."
<p>The data used in correspondence on the article entitled “Reply: Correspondence on NanoVar’s performance outlined by Jiang T. et al. in ‘Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation’.”. It contains the benchmarking results evaluated by Truvari. The running log files of NanoVar are also included in this repository.</p>
Comprehensive Program to Improve Reading and Writing Skills in At-Risk and Dyslexic Children
ClinicalTrials.gov study NCT00061412. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Seq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
<p>Annotation of full-length scFvs sequenced with PacBio using Seq2scFv (https://github.com/ngs-ai-org/seq2scfv). </p> <p>Raw files were obtained from publicly available dataset generated by Nannini and colleagues in "Combining phage display with SMRTbell next-generation sequencing for the rapid discovery of functional scFv fragments." <em>MAbs</em>. Vol. 13. No. 1. Taylor & Francis, 2021.</p> <p>The results of the annotation are organized in directories. These correspond to the different steps of the tutorial presented in the Seq2scFv repository. </p> <p>├── 1.Preprocessed<br>├── 2.Catalogued<br>├── 3.vscan<br>├── 4.scFv_split<br>├── 5.Linkers<br>├── 6.Flags<br>├── 7.Counts<br>└── focus_libs.txt</p> <p>This entry also contains the code provided in the GitHub repository.</p>
Comprehensive long-read transcriptomic analysis reveals multi-level transcriptional alterations mediated by miR-214-3p dysregulation in gastric cancer cells
GEO Series GSE300926. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Effect of Music on Reading Comprehension in Patients With Aphasia
ClinicalTrials.gov study NCT03600987. IPD Sharing: NO. Countries: 1. Publications: 0.
Parents Reading Comprehension of Their Child's Post-Operative Medicine Fact Sheets
ClinicalTrials.gov study NCT00639470. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Noninvasive Brain Stimulation to Enhance Reading Comprehension Ability in Adults
ClinicalTrials.gov study NCT05523505. IPD Sharing: YES. Countries: 1. Publications: 0.
Effect of Music on Reading Comprehension for Patients With Aphasia
ClinicalTrials.gov study NCT02875938. IPD Sharing: NO. Countries: 1. Publications: 0.
Comprehensive characterization of transcript isoform in mouse retina with ONT long read single-cell RNA sequencing
GEO Series GSE255520. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
The Effect of Washback on Reading Comprehension
ClinicalTrials.gov study NCT01642316. IPD Sharing: Not stated. Countries: 0. Publications: 0.
Comprehensive long-read transcriptome analysis uncovers alternative RNA processing feature and isoform diversity in ovarian cancer progression
GEO Series GSE315136. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive transcriptome characterization deciphers mechanisms underpinning the positive selection of B cells in germinal centers. [mouse; short-read]
GEO Series GSE278742. Mus musculus. 20 samples. Type: Expression profiling by high throughput sequencing.
ORCA. IT: a new web-based tool for assessing online reading search and comprehension abilities in students reveals effects of gender, school type and reading ability. Frontiers in psychology, 10, 2433.
<p>Dataset containing the raw scores of the participants described in the paper "ORCA. IT: a new web-based tool for assessing online reading search and comprehension abilities in students reveals effects of gender, school type and reading ability", published in <em>Frontiers in Psychology</em>, <em>10</em>, 2433.</p>
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.