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4 results for “Inferelator”
Inferelator Saccharomyces Cerevisiae Data Set
<p>This data is associated with the Inferelator package. It consists of an expression data set, a prior data matrix generated from ATAC-seq data, and a gold standard derived from YEASTRACT. It was initially used in Tchourine, K., Vogel, C., and Bonneau, R. (2018). Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. Cell Reports 23, 376–388.</p>
Inferelator Saccharomyces Cerevisiae Single-Cell Data Set
<p>This data is associated with the Inferelator package. It has an expression data set (103118_SS_Data.tsv.gz), which is a [Cells x Genes] TSV file which has 5 included metadata columns [Genotype, Genotype_Group, Replicate, Condition, tenXBarcode]. It also contains a prior data matrix generated from the YEASTRACT database (YEASTRACT_Both_20181118.tsv), a gold standard derived from the YEASTRACT database (gold_standard.tsv), a list of transcription factors (tf_names_restrict.tsv), and a list of protein-coding genes (orfs.tsv). It was initially used in Jackson, C.A., Castro, D.M., Saldi, G.-A., Bonneau, R., and Gresham, D. (2019). Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments. BioRxiv 581678.</p>
Inferelator Example Data and Scripts
<p>This archive contains example data associated with the Inferelator python package. Included is yeast microarray gene expression data initially used in Tchourine et al (2018). Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks (Cell Reports 23, 376–388). Also included is yeast single-cell gene expression data initially used in Jackson & Castro et al (2019). Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments (BioRxiv 581678). Also included is bacillus microarray gene expression data initially used in Arrieta‐Ortiz et al (2015). An experimentally supported model of the Bacillus subtilis global transcriptional regulatory network (Molecular Systems Biology 11, 839).</p> <p>This archive also contains example scripts for basic network inference on all three of these data sets. </p> <p> </p> <p> </p>
Inferelator 3.0 Yeast Single-Cell Benchmarking Data
<p>Yeast single-cell gene expression data, database-derived prior knowledge network, and hand-curated gold standard network. Used to benchmark the Inferelator 3.0, SCENIC, and CellOracle.</p> <p>Expression data (GSE144820_GSE125162.tsv.gz) is an integer count matrix [44343 rows x 6763 columns] with an index column (0) assembled from <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144820">GSE144820</a> and <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE125162">GSE125162</a>. Included is a paired metadata file (GSE144820_GSE125162_META_DATA.tsv.gz).</p> <p>A database-derived prior knowledge network (YEASTRACT_20190713_BOTH.tsv) is a boolean connectivity matrix [6885 rows x 220 columns] with an index column (0) obtained from the <a href="http://www.yeastract.com/">YEASTRACT</a> database on 07132019. It consists of edges which have both DNA localization evidence and evidence of changes to gene expression after TF perturbation.</p> <p>A curated gold standard network (Tchourine_2018_yeast_gold_standard.tsv) is a signed connectivity matrix [993 rows x 98 columns] with an index column (0). <a href="https://pubmed.ncbi.nlm.nih.gov/29641998/">Details of its construction have been published</a>.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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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.