Man pages for maehrlab/thymusatlastools
Tools for analysis of single-cell transcriptomic data

add_cc_scoreQuantify cell-cycle activity by phase.
add_maehrlab_metadataGiven a Seurat object, add information about our experiments.
add_pseudotime_to_seuratTransfer data from a pseudotime modeling object to a Seurat...
add_quadrantsSplit a scatterplot (or similar) into quadrants and label...
add_rp_mt_percentageQuantify ribosomal and mitochondrial transcript content cell...
add_rp_percentageQuantify ribosomal transcript content cell by cell.
add_tcrAdd T-cell receptor expression from a separate alignment...
aggregate_niceAggregate data.frame by a categorical variable, permissively.
align_embedding_to_referenceAlign simple (y-shaped) lineage trees represented as points...
annot_ident_plotAnnotate a plot with cluster labels
are_compatibleHelper function. Check if a list of markers is compatible...
AvailableDataGet available variable names (genes, identity classes, PCA...
call_monocle_on_seuratExtract data from a Seurat object and run Monocle, returning...
check_xist_allScreen for female embryos using simple stats.
check_xist_pureCheck for female-specific and male-specific transcripts
classify_mlrApply a machine learning classifier (from...
ClusterBagApply a bagged clustering procedure to a Seurat object using...
ClusterBagStabilityWrapper for ClusterBag. Measures stability over a range of...
cluster_wrapperA wrapper for Seurat's clustering functions.
collapse_by_nameTurn a named list or vector of strings into a pipe-separated...
convert_species_dgeConvert a raw digital gene expression matrix from one species...
custom_feature_plotMake tSNE plots (or PCA, or Monocle; it's customizable)
custom.make.uniqueConsistently label replicates
dendrogram_merge_pointsPlot a dendrogram and also cut it to merge input into...
deseuratify_raw_dataExtract mostly-raw (medium rare?) data from a Seurat object.
DESummaryFastQuickly compute summary statistics for all genes.
dge_merge_listMerge a list of digital gene expression matrices.
dir.create.niceCreate new directories recursively and without a warning if...
do_enrichrProgrammatically feed gene-sets to Enrichr and save formatted...
expected_doublet_countsGiven a named vector x with counts of various cell types,...
explore_embeddingsQuickly explore many parameter settings
ExploreIterativelyExplore a single-cell dataset, alternating between gene...
export_from_seuratExport raw and normalized data from a Seurat object.
faceted_tsnePlot a dataset's tSNE embedding faceted by experimental...
facet_plot_gene_clustersDraw overlaid line plots of gene clusters from output of...
FetchDataZeroPadFetchData but with zeroes for unavailable genes
FillNARemove missing values from the metadata, issuing a warning if...
FindMarkersFlexTest for markers flexibly from a Seurat object.
fix_cluster_orderCheck if a list of cell types is good to be used to order...
get_classifier_coefsExtract coefficients from a glmnet multiclass logistic...
get_cTEC_mTEC_genesReturn a table of genes generated by head-to-head comparison...
get_macosko_cc_genesReturn cell-cycle genes from original Drop-seq paper by...
get_metadataGet thymus atlas sample metadata.
get_mouse_tfsMaehr lab list of mouse transcription factors.
get_orthologReturn the ortholog of a given gene or NA (if no match)....
get_ortholog_nonvecReturn the ortholog of a given gene or NA (if no match). Not...
get_ortholog_tableHuman-mouse ortholog pairs from Ensembl 87.
get_poised_genesPoised genes from Lesch 2016 Nature Genetics
get_preimageTake in a function from one finite set of strings to another...
get_ramilowskiReturn human receptor-ligand pairs from Ramilowski et al...
get_rene_markersReturn df with handpicked genes.
get_similar_genesFind genes with expression patterns similar to the genes...
harmonize_speciesGiven a gene list and a seurat object, return a gene list...
has_orthologSame as get_ortholog but returns just T or F.
heatmap_gene_clustersDraw heatmaps of gene clusters from output of...
is_mtDecide if genes are mitochondrial. Currently uses a crude...
is_rpDecide if a gene is a ribosomal subunit or a pre-rRNA...
KMeansGapStatImitate Seurat::FindClusters but using k-means with the gap...
knn_classifierClassify cells from one Seurat object in terms of another...
load_thymus_profiling_dataLoad digital gene expression matrices from Maehrlab dropbox.
make_heatmap_for_tableMake a heatmap with one column for each cluster in 'unique(...
master_ptRun Monocle, DPT, or PCA-based pseudotime analysis on a...
misc_summary_infoSave commonly needed summary plots: plain gray, eday,...
normalize_cpx_amtRescale every cell to a certain amount of UMIs, where that...
outlier_labeled_scatterplotReturn a scatterplot, labeling outliers.
pc_as_ptTake a principal component (first by default) and return a...
plot_dendro_with_rectPlot a dendrogram, labeling merges given by 'converter' with...
ProjectCellsProject cells from one Seurat object onto the pseudotime axis...
RefineVariableGenesUpdate the '@var.genes' slot of a Seurat object using cluster...
remove_species_specific_genesRemove species-specific genes from a Seurat object.
remove_TEC_doubletsRemove intra-TEC doublets by finding cells with both a high...
replace_with_int_rankConvert a, b, b, a, c, a to 1, 2, 2, 1, 3, 1. Works with any...
SanitizeGenesSanitize gene names via 'make.names'
save_depth_statsAssemble very basic summary stats: total UMIs, genes, and...
save_feature_plotsSave plots en masse.
save_marker_tableClean and save a df containing columns "gene", "avg_diff",...
seuratify_thy_dataMake arrays into Seurat objects.
SeuratMergeMerge two Seurat objects.
SeuratPieMake small-multiple pie charts.
smooth_and_cluster_genesCharacterize genes by behavior over pseudotime, returning...
strip_suffixRemove a suffix if it is present, but if it's absent, avoid...
strsplit_dropWrap base::strsplit with a 'drop' option
SubsetDataFlexSubset data flexibly from a Seurat object.
TACSMake a FACS-like plot from a single-cell rna-seq dataset.
text2fileWrite text to a file
time_seriesReturn spline-smoothed expression plots over pseudotime.
time_series_saveSave plots from 'times_series'.
train_save_classifierTrain and save a penalized logistic regression classifier.
tsne_coloredSave plots from 'custom_feature_plot'.
wheel_plotVisualize probabilistic classification results
maehrlab/thymusatlastools documentation built on June 1, 2018, 10:09 a.m.