Single Cell RNAseq of Mouse Testis

<p>This is the processed data from the publication:&nbsp;&quot;Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains&quot; (https://doi.org/10.1101/393769)</p> <p>The raw data is avaliable at GEO:&nbsp;GSE113293</p> <p>Associated software is at&nbsp;https://zenodo.org/badge/latestdoi/140632831</p> <p>SDA_objects.zip contains key tables required for many functions, download this to use the shiny app. Contents:</p> <ul> <li>cell_data: data.table containing metadata of the cells. 80 columns including cell id, SDA component cell scores, Tsne coordinates, pseudotime, experimental group etc.</li> <li>data: a sparse matrix of normalised read counts (20322 cells by 19262 genes)</li> <li>gene_annotations: data.table containing gene locations, enrichment vs other tissues from bulk data, infertility gene status</li> <li>GO_enrich: data.table containing gene ontology enrichments for each component, the genes enriched, p.values and enrichment values</li> <li>principal_curves: list of output of princurve() containing the pseudotime trajetories</li> <li>SDAresults: output of SDA run loaded using SDAtools::load_results()</li> </ul> <p>Other R objects include:</p> <ul> <li>QC_count_matrix: Sparse matrix of raw count values for QC cells and genes</li> <li>cell_imputation_AUCs: data.table of PRAC AUC values for unimputed (train), mean cell, SDA (predict), ICA, PCA, NNMF, and MAGIC</li> <li>HocomocoV11_motifProbs_matrix: Matrix of regulation probabilities from MotifFinder using fixed motifs from HocomocoV11 database</li> <li>motifFinder_denovo: list of results of MotifFinder denovo motifs from promoters regions of genes from each component</li> <li>motifFinder_denovo_fixed: list of results of MotifFinder using 125 denovo motifs with fixed motif on all genes.</li> <li>tomtom_matched_motifs: data.table of TOMTOM matches of denovo motifs, plus metadata</li> </ul>