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4 results for “Motif discovery”
Neural motif discovery manuscript reports
<p>This repository holds the supplementary data for the motif and motif-syntax/grammar discovery tool in the associated manuscript.</p> <p><strong>reports.tar.gz</strong><br> Contains the motif and motif-syntax/grammar analysis reports as HTML files for all analyzed transcription factors (TFs). See included README for more details.</p> <p><strong>models.tar.gz</strong><br> Contains the fine-tuned models. Each TF, this includes the fine-tuned single-task profile model for each task/experiment, and the fine-tuned multi-task profile model over all experiments.</p> <p><strong>motifs.tar.gz</strong><br> Contains the motifs discovered by TF-MoDISco on each profile model, for both the profile and counts heads. This includes the PFM, the CWM, and eCWM. This also includes the motifs that have been merged across the profile/counts heads (i.e. `cpmerged`).</p> <p><strong>motif_hits.tar.gz</strong><br> For each experiment, motif instances were called using FiNeMo on the best-performing model. Motif instances are either called for the profile head, count head, or merged across both heads. Each subdirectory includes: 1) the collapsed and filtered motif instances; 2) the set of peaks for which they come from; 3) a file matching motif instances to their peaks; 4) the co-occurrence of multiple motifs in peaks; and 5) the distance distribution of motif pairs which significantly co-occur. Unless stated otherwise, collapsing is done over all motif patterns.</p>
Dataset associated with the study titled "Systematic discovery of regulatory motifs associated with human insulator sites" It includes data used for predicting insulator-associated DNA-binding proteins.
<p><strong>This dataset was used in the study on the prediction of insulator-associated DNA-binding proteins.</strong></p> <p>The three files included here are intended for use with the code available in the following GitHub repository:<br><a href="https://github.com/reposit2/insulator" target="_new" rel="noopener">https://github.com/reposit2/insulator</a></p> <p>To use the data, extract all three files and place them in the same directory as the code files.</p>
CENTDIST: Discovery of Co-associated Factors by Motif Distribution
GEO Series GSE28857. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
SHAPE-guided RNA structure homology search and motif discovery
GEO Series GSE189259. Severe acute respiratory syndrome-related coronavirus; Severe acute respiratory syndrome coronavirus 2. 4 samples. Type: Other.
ScienceDex guides
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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.