audit_sample_missing_publication

audit_file_set_missing_publication

audit_file_set_files_missing_analysis_step_version

Andrew Allen

Design, prediction, and prioritization of systematic perturbations of the human genome

Predictions of mutation effect at every base in ENCODE cCREs across hg38.

Bill Majoros, Duke

virtual Homo sapiens (female) K562 cell line

functional effect prediction on scope of loci

Predictions of mutation effect at every based in ENCODE cCREs across hg38, merged from 1064 chunks

audit_input_file_sets_derived_from

BlueSTARR v0.1.1 is the updated version that was trained on a full-set dataset containing sequences from all chromosomes, unlike the original model (v0.1.0), which excluded chromosomes 1 and 2 for testing and validation. It uses DNA and RNA counts normalized by library size, employs unbiased down-sampling for training, and optimizes predictions using Mean Squared Error (MSE) as the loss function

BlueSTARR-K562 v0.1.1 neural network predicting regulatory elements

BlueSTARR is a neural network trained on STARR-seq data that takes genomic sequence as input and predicts STARR-seq activity as output.  This version of BlueSTARR was trained on a STARR-seq experiment done in K562 cells, and takes a 300 bp sequence as input.  Variant predictions are made by running the model twice (once for the reference allele and once for the alternate allele) and computing the predicted log2 fold change in STARR-seq activity for the change from reference to alternate.

BlueSTARR-K562 v0.1.0 neural network predicting regulatory elements

Accession

Aliases

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Assay Term

Assemblies

Assessed Genes

Associated Phenotypes

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Data Use Limitation Summaries

Description

Donors

Taxa

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Measured Mechanism

Input File Sets

Measurement Sets

Model Name

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Preferred Assay Title

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Simplified Sample Summary

Samples

Sample Institutional Certificates

Sample Summary

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Selection Criteria

Sequencing Library Types

Genes

Status

Summary

Assay Targeted Genes

Transcriptome Annotations

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Object Type

Classification

Sample

File Format

Data Use Limitation

Audit category: NOT COMPLIANT

Audit category: WARNING

Audit Category: Internal Action

Externally Hosted

samples.@id

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