| add_binary_states | Add binary state information to the scd. |
| add_clonotype_annotations | Add VDJ information using some code I found. |
| add_conditional_nas | Replace 0 with NA if not all entries for a given condition... |
| all_adjusters | Combine all surrogate estimators and batch correctors into... |
| all_gprofiler | Run simple_gprofiler on every table from... |
| all_ontology_searches | Perform ontology searches given the results of a differential... |
| all_pairwise | Perform limma, DESeq2, EdgeR pairwise analyses. |
| annotate_network | Use grep to add a vector of annotations/colors to a network. |
| annotate_network_df | A version of annotate_network, but which uses a dataframe as... |
| annotation-expt-method | A getter for the annotation databased used to create an... |
| annotation-set-expt-ANY-method | A setter for the annotation database used to create an... |
| assay-ExpressionSet-ANY-method | A getter to pull the assay data from an ExpressionSet. |
| assay-expt-ANY-method | A getter to pull the assay data from an expt. |
| assay-set-ExpressionSet-ANY-method | A setter to put the assay data into an ExpressionSet. |
| assay-set-expt-ANY-method | A setter to put the assay data into an expt. |
| backup_expression_data | Keep a copy of the original state of an expressionset in case... |
| backup_expression_data-ExpressionSet-method | Backup the state of an expressionSet. |
| backup_expression_data-SummarizedExperiment-method | Backup the state of an SummarizedExperiment. |
| backup_file | Make a backup of an existing file with n revisions, like VMS! |
| base_size | The following sets the ggplot2 default text size. |
| basic_pairwise | The simplest possible differential expression method. |
| batch_counts | Perform different batch corrections using limma, sva, ruvg,... |
| binary_pairwise | Perform all_pairwise only using deseq/edger. |
| bioc_all | Grab a copy of all bioconductor packages and install them by... |
| calculate_aucc | Calculate the Area under the Concordance Curve. |
| cbcb_batch | A function suggested by Hector Corrada Bravo and Kwame Okrah... |
| cbcb_combat | A modified version of comBatMod. |
| cbcb_filter_counts | Filter low-count genes from a data set using cpm data and a... |
| cheap_tm | Simplified TM calculator |
| check_circos | Validation function when creating a circos class. |
| check_includes | Convert a vector of yes/no by DE method to a list. |
| check_metadata_year | Figure out when mappings were performed by their timestamp |
| check_plot_scale | Look at the range of the data for a plot and use it to... |
| check_xlsx_worksheet | Create the named worksheet in a workbook, this function was... |
| choose_basic_dataset | Attempt to ensure that input data to basic_pairwise() is... |
| choose_binom_dataset | A sanity check that a given set of data is suitable for... |
| choose_dataset | Choose a suitable data set for Edger/DESeq |
| choose_limma_dataset | A sanity check that a given set of data is suitable for... |
| choose_model | Try out a few experimental models and return a likely working... |
| choose_sequence_regions | Given a named vector of fun regions, make a dataframe which... |
| circos_arc | Write arcs between chromosomes in circos. |
| circos_check_chromosomes | Make sure I haven't mixed and matched genomes. |
| circos-class | Create a class for circos data |
| circos_heatmap | Write tiles of arbitrary heat-mappable data in circos. |
| circos_hist | Write histograms of arbitrary floating point data in circos. |
| circos_ideogram | Create the description of chromosome markings. |
| circos_karyotype | Create the description of (a)chromosome(s) for circos. |
| circos_make | Write a simple makefile for circos. |
| circos_plus_minus | Write tiles of bacterial ontology groups using the categories... |
| circos_prefix | Write the beginning of a circos configuration file. |
| circos_suffix | Write the end of a circos master configuration. |
| circos_ticks | Create the ticks for a circos plot. |
| circos_tile | Write tiles of arbitrary categorical point data in circos. |
| classify_n_times | Rerun a model generator and classifier on a training/testing... |
| classify_variants | Given a pile of variants from freebayes and friends, make a... |
| clear_session | Clear an R session, this is probably unwise given what I have... |
| cleavage_histogram | Make a histogram of how many peptides are expected at every... |
| cluster_trees | Take clusterprofile group data and print it on a tree as per... |
| colData-ExpressionSet-method | A getter to pull the sample data from an ExpressionSet. |
| colData-expt-method | A getter to pull the sample data from an expt. |
| colData-set-ExpressionSet-ANY-method | A setter to put the sample data into an ExpressionSet. |
| colData-set-expt-ANY-method | A setter to put the sample data into an expt. |
| color_int | Translate the hexadecimal color codes to three decimal... |
| colors | Get the colors from an expt. |
| colors-expt-method | A getter to pull the colors from an expt. |
| colors-set | Set the colors to an expt. |
| colors-set-expt-method | A setter to put the colors into an expt. |
| colors-set-SummarizedExperiment-method | A setter to put the colors into a SummarizedExperiment. |
| colors-SummarizedExperiment-method | A getter to pull the colors from a SummarizedExperiment. |
| column_assignment | data.table's funky column assignment operator |
| combine_de_tables | Combine portions of deseq/limma/edger table output. |
| combine_expts | Take two expressionsets and smoosh them together. |
| combine_extracted_plots | Gather data required to make MA/Volcano plots for pairwise... |
| combine_mapped_table | Combine data taken from map_keepers() into a single large... |
| combine_single_de_table | Given a limma, edger, and deseq table, combine them into one. |
| compare_batches | Attempt to compare the results from the various batch/sv... |
| compare_de_results | Compare the results of separate all_pairwise() invocations. |
| compare_de_tables | Use plot_linear_scatter to compare to de tables. |
| compare_go_searches | Compare the results from different ontology tools |
| compare_logfc_plots | Compare logFC values from limma and friends |
| compare_pc_sv | Incomplete function to compare PCs and SVs. |
| compare_significant_contrasts | Implement a cleaner version of 'subset_significants' from... |
| compare_surrogate_estimates | Perform a comparison of the surrogate estimators demonstrated... |
| concatenate_runs | Sum the reads/gene for multiple sequencing runs of a single... |
| convert_counts | Perform a cpm/rpkm/whatever transformation of a count table. |
| convert_gsc_ids | Use AnnotationDbi to translate geneIDs from type x to type y. |
| convert_ids | Change gene IDs to the format expected by gsva using an... |
| cordist | Similarity measure which combines elements from Pearson... |
| correlate_de_tables | See how similar are results from limma/deseq/edger/ebseq. |
| count_clonotype_by_cluster | Add a df of clonotype observations by cell cluster to @misc... |
| count_expt_snps | Gather snp information for an expt |
| count_nmer | Count n-mers in a given data set using Biostrings |
| count_nmer-character-method | Count nmers given a filename instead of genome object. |
| counts_from_surrogates | A single place to extract count tables from a set of... |
| cp_options | Set up appropriate option sets for clusterProfiler |
| create_expt | Wrap bioconductor's expressionset to include some extra... |
| create_partitions | Use createDataPartition to create test/train sets and massage... |
| create_scd | Create a combined seurat object from a sample sheet. |
| create_se | Create a SummarizedExperiment given some metadata |
| default_proper | Invoke PROPER and replace its default data set with data of... |
| deparse_go_value | Extract more easily readable information from a GOTERM datum. |
| deseq2_pairwise | Set up model matrices contrasts and do pairwise comparisons... |
| deseq_lrt | Bring together some of the likelihood ratio test analyses. |
| deseq_pairwise | deseq_pairwise() Because I can't be trusted to remember '2'. |
| deseq_try_sv | Given a set of surrogate variables from sva and friends, try... |
| de_venn | Create venn diagrams describing how well deseq/limma/edger... |
| disjunct_pvalues | Test for infected/control/beads - a placebo effect? |
| dispatch_count_lines | Count the number of lines in an input file spec and add it to... |
| dispatch_csv_search | Pull some information from a csv/tsv file. |
| dispatch_fasta_lengths | Get the lengths of sequences from a fasta file. |
| dispatch_filename_search | Pull out the filename matching an input spec |
| dispatch_gc | Pull GC content into the metadata sheet. |
| dispatch_metadata_extract | This is basically just a switch and set of regexes for... |
| dispatch_metadata_ratio | Given two metadata columns, print a ratio. |
| dispatch_regex_search | Generic dispatcher to hunt down useful information from logs. |
| divide_seq | Express a data frame of counts as reads per pattern per... |
| do_batch | Actually runs the batch method, this more than anything shows... |
| do_pairwise | Generalize pairwise comparisons |
| dopar | dopar |
| dot-data | Taken from Nathan Eastwood to help using mutate and friends. |
| do_topgo | An attempt to make topgo invocations a bit more standard. |
| download_gbk | A genbank accession downloader scurrilously stolen from ape. |
| download_microbesonline_files | Download the various file formats from microbesoline. |
| dream_pairwise | Set up a model matrix and set of contrasts for pairwise... |
| ebseq_few | Invoke EBMultiTest() when we do not have too many conditions... |
| ebseq_pairwise | Set up model matrices contrasts and do pairwise comparisons... |
| ebseq_pairwise_subset | Perform pairwise comparisons with ebseq, one at a time. |
| ebseq_size_factors | Choose the ebseq normalization method to apply to the data. |
| ebseq_two | The primary function used in my EBSeq implementation. |
| edger_pairwise | Set up a model matrix and set of contrasts to do pairwise... |
| enrichResult | The enrichResult class. |
| exclude_genes_expt | A temporary alias to subset_genes |
| exprs-expt-method | A getter to pull the expression data from an expt. |
| exprs-set-ExpressionSet-data.frame-method | A setter to put the expression data into an expt. |
| exprs-set-expt-ANY-method | A setter to put the expression data into an expt. |
| exprs-set-SummarizedExperiment-ANY-method | A setter to put the expression data to a... |
| exprs-SummarizedExperiment-method | A getter to pull the expression data from a... |
| expt | An expt is an ExpressionSet superclass with a shorter name. |
| extract_abundant_genes | Extract the sets of genes which are significantly more... |
| extract_coefficient_scatter | Perform a coefficient scatter plot of a... |
| extract_de_plots | Make a MA plot of some limma output with pretty colors and... |
| extract_go | Extract a set of geneID to GOID mappings from a suitable data... |
| extract_interesting_goseq | Filter a goseq significance search |
| extract_keepers | When a list of 'keeper' contrasts is specified, extract it... |
| extract_lengths | Take gene/exon lengths from a suitable data source... |
| extract_mayu_pps_fdr | Read output from mayu to get the IP/PP number corresponding... |
| extract_metadata | Pull metadata from a table (xlsx/xls/csv/whatever) |
| extract_msraw_data | Read a bunch of mzXML files to acquire their metadata. |
| extract_mzML_scans | Parse a mzML file and return the relevant data. |
| extract_mzXML_scans | Parse a mzXML file and return the relevant data. |
| extract_peprophet_data | Get some data from a peptideprophet run. |
| extract_pyprophet_data | Read a bunch of scored swath outputs from pyprophet to... |
| extract_scan_data | Read a mzML/mzXML file and extract from it some important... |
| extract_siggenes | Alias for extract_significant_genes because I am dumb. |
| extract_significant_genes | Extract the sets of genes which are significantly up/down... |
| factor_rsquared | Collect the r^2 values from a linear model fitting between a... |
| fData-expt-method | A getter to pull the gene annotation data from an expt. |
| fData-set-expt-ANY-method | A setter to put the gene annotation data into an expt. |
| fData-set-SummarizedExperiment-ANY-method | A setter to put the gene annotation data into a... |
| fData-SummarizedExperiment-method | A getter to pull the gene annotation data from a... |
| features_greater_than | Count the number of features(genes) greater than x in a data... |
| features_in_single_condition | I want an easy way to answer the question: what features are... |
| features_less_than | Do features_greater_than() inverted! |
| filter_counts | Call various count filters. |
| filter_scd | Perform a series of filters on a single-cell dataset. |
| find_subseq_target_temp | Find a subsequence with a target PCR temperature. |
| find_working_dataset | Search a mart for a usable dataset. |
| find_working_mart | Find a functional biomart instance. |
| flanking_sequence | Extract sequence flanking a set of annotations (generally... |
| gather_cp_genes | Collect gene IDs from a table and make them readable. |
| gather_eupath_utrs_padding | Given an eupathdb species lacking UTR boundaries, extract an... |
| gather_genes_orgdb | Use the orgdb instances from clusterProfiler to gather... |
| gather_masses | Use BRAIN to find the peptide mass from a sequence. |
| gather_ontology_genes | Given a set of goseq data from simple_goseq(), make a list of... |
| gather_preprocessing_metadata | Automagically fill in a sample sheet with the results of the... |
| gather_utrs_padding | Take a BSgenome and data frame of chr/start/end/strand,... |
| gather_utrs_txdb | Get UTR sequences using information provided by TxDb and... |
| genefilter_cv_counts | Filter genes from a dataset outside a range of variance. |
| genefilter_kofa_counts | Filter low-count genes from a data set using genefilter's... |
| genefilter_pofa_counts | Filter low-count genes from a data set using genefilter's... |
| generate_expt_colors | Set up default colors for a data structure containing usable... |
| generate_nn_groups | Given an n-dimensional matrix, try some KNN-esque clustering... |
| genomic_kmer_dist | Use ape to generate a distance based nj tree from fasta... |
| genoplot_chromosome | Try plotting a chromosome (region) |
| get_abundant_genes | Find the set of most/least abundant genes according to limma... |
| get_backup_expression_data | Extract the backup copy of an expressionset from an expt. |
| get_backup_expression_data-ExpressionSet-method | Get the backup data from an ExpressionSet. |
| get_backup_expression_data-SummarizedExperiment-method | Get the backup data from a SummarizedExperiment. |
| getEdgeWeights | Plot the ontology DAG. |
| get_expt_colors | Get a named vector of colors by condition. |
| get_genesizes | Grab gene length/width/size from an annotation database. |
| get_git_commit | Get the current git commit for hpgltools |
| get_group_gsva_means | Create dataframe which gets the maximum within group mean... |
| get_gsvadb_names | Extract the GeneSets corresponding to the provided name(s). |
| get_identifier | Get an Identifier function from a shorthand name. |
| get_individual_snps | Extract the observed snps unique to individual categories in... |
| get_kegg_compounds | Gather all Compounds from all pathways for a given species. |
| get_kegg_genes | Extract the set of geneIDs matching pathways for a given... |
| get_kegg_orgn | Search KEGG identifiers for a given species name. |
| get_kegg_sub | Provide a set of simple substitutions to convert geneIDs from... |
| get_microbesonline_taxid | Extract microbesonline taxon IDs without having to click on... |
| get_msigdb_metadata | Create a metadata dataframe of msigdb data, this hopefully... |
| get_pairwise_gene_abundances | A companion function for get_abundant_genes() |
| get_plot_columns | A small rat's nest of if statements intended to figure out... |
| get_proportion_snp_sets | Create all possible sets of variants by sample (types). |
| get_res | Attempt to get residuals from tsne data |
| get_sig_genes | Get a set of up/down differentially expressed genes. |
| get_sig_gsva_categories | Attempt to score the results from simple_gsva() |
| get_snp_sets | Collect variants associated with specific conditions. |
| get_yyyymm_commit | Find the git commit closest to the given yyyymmdd. |
| gff2gr | Rewrite a gff file as a granges with full seqinfo if... |
| gff2irange | Extract annotation information from a gff file into an irange... |
| ggplotly_url | Add a little logic to ggplotly to simplify adding clicky... |
| ggplt | Simplify plotly ggplot conversion so that there are no... |
| godef | Get a go long-form definition from an id. |
| golev | Get a go level approximation from an ID. |
| golevel | Get a go level approximation from a set of IDs. |
| golevel_df | Extract a dataframe of golevels using getGOLevel() from... |
| goont | Get a go ontology name from an ID. |
| gosec | Get a GO secondary ID from an id. |
| goseq2enrich | Create a clusterProfiler compatible enrichResult data... |
| goseq_msigdb | Pass MSigDB categorical data to goseq and run it. |
| goseq_table | Enhance the goseq table of gene ontology information. |
| goseq_trees | Make fun trees a la topgo from goseq data. |
| gostats2enrich | Create a clusterProfiler compatible enrichResult data... |
| gostats_kegg | Use gostats() against kegg pathways. |
| gostats_trees | Take gostats data and print it on a tree as topGO does. |
| gosyn | Get a go synonym from an ID. |
| goterm | Get a go term from ID. |
| gotest | Test GO ids to see if they are useful. |
| gprofiler2enrich | Recast gProfiler data to the output class produced by... |
| grapes-colon-colon-colon-grapes | R CMD check is super annoying about :::. |
| graph_metrics | Make lots of graphs! |
| group_mean_cds_length | Average the cds length over known transcripts for a single... |
| guess_orgdb_keytype | Iterate over keytypes looking for matches against a set of... |
| heatmap.3 | a minor change to heatmap.2 makes heatmap.3 |
| hpgl_arescore | Implement the arescan function in R |
| hpgl_cor | Wrap cor() to include robust correlations. |
| hpgl_dist | Because I am not smart enough to remember t() |
| hpgl_filter_counts | Filter low-count genes from a data set using cpm data and a... |
| hpgl_GOplot | A minor hack of the topGO GOplot function. |
| hpgl_GroupDensity | A hack of topGO's groupDensity() |
| hpgl_log2cpm | Converts count matrix to log2 counts-per-million reads. |
| hpgl_norm | Normalize a dataframe/expt, express it, and/or transform it |
| hpgl_padjust | Wrap p.adjust to add IHW adjustments as an option. |
| hpgl_qshrink | A hacked copy of Kwame's qsmooth/qstats code. |
| hpgl_qstats | A hacked copy of Kwame's qsmooth/qstats code. |
| hpgl_rpkm | Reads/(kilobase(gene) * million reads) |
| hpgltools | hpgltools: a suite of tools to make our analyses easier |
| hpgl_voom | A slight modification of limma's voom(). |
| hpgl_voomweighted | A minor change to limma's voom with quality weights to... |
| iDA | Generic method to input data to iDA |
| iDA-matrix-method | Set method for matrix to input data to iDA |
| ihw_adjust | Make sure the outputs from limma and friends are in a format... |
| import_deseq | Try to add data to DESeq in a flexible fashion. This... |
| import_edger | Import tximport information into edgeR. |
| impute_expt | Impute missing values using code from DEP reworked for... |
| init_xlsx | Initialize an xlsx file with a little bit of logic to make... |
| intersect_signatures | Take a result from simple_gsva(), a list of gene IDs, and... |
| intersect_significant | Find the sets of intersecting significant genes |
| kegg_vector_to_df | Convert a potentially non-unique vector from kegg into a... |
| limma_pairwise | Set up a model matrix and set of contrasts for pairwise... |
| load_annotations | Use one of the load_*_annotations() functions to gather... |
| load_biomart_annotations | Extract annotation information from biomart. |
| load_biomart_go | Extract gene ontology information from biomart. |
| load_biomart_orthologs | Use biomart to get orthologs between supported species. |
| load_genbank_annotations | Given a genbank accession, make a txDb object along with... |
| load_gff_annotations | Extract annotation information from a gff file into a df |
| load_gmt_signatures | Load signatures from either a gmt file, xml file, or directly... |
| load_kegg_annotations | Create a data frame of pathways to gene IDs from KEGGREST |
| loadme | Load a backup rdata file |
| load_microbesonline_annotations | Skip the db and download all the text annotations for a given... |
| load_microbesonline_go | Extract the set of GO categories by microbesonline locus |
| load_orgdb_annotations | Load organism annotation data from an orgdb sqlite package. |
| load_orgdb_go | Retrieve GO terms associated with a set of genes. |
| load_trinotate_annotations | Read a csv file from trinotate and make an annotation data... |
| load_trinotate_go | Read a csv file from trinotate and extract ontology data from... |
| load_uniprot_annotations | Download the txt uniprot data for a given accession/species. |
| load_uniprot_go | Extract ontology information from a uniprot dataframe. |
| local_get_value | Perform a get_value for delimited files |
| make_assembly_spec | Generate an assembly annotation specification for use by... |
| make_dnaseq_spec | Generate a DNASeq specification for use by... |
| make_gsc_from_abundant | Given a pairwise result, make a gene set collection. |
| make_gsc_from_ids | Create a gene set collection from a set of arbitrary IDs. |
| make_gsc_from_pairwise | Given a pairwise result, make a gene set collection. |
| make_id2gomap | Make a go mapping from IDs in a format suitable for topGO. |
| make_kegg_df | Use pathfindR to get a dataframe of KEGG IDs. |
| make_limma_tables | Writes out the results of a limma search using toptable(). |
| make_pairwise_contrasts | Run makeContrasts() with all pairwise comparisons. |
| make_pombe_expt | Create a Schizosaccharomyces cerevisiae expt. |
| make_pombe_se | Analagous function to make_pombe_expt() |
| make_rnaseq_spec | Generate a RNASeq specification for use by... |
| make_simplified_contrast_matrix | Create a contrast matrix suitable for MSstats and similar... |
| make_tx_gene_map | I keep messing up the creation of the salmon trancript to... |
| map_keepers | Find the correct tables given a set of definitions of desired... |
| map_kegg_dbs | Maps KEGG identifiers to ENSEMBL gene ids. |
| map_orgdb_ids | Map AnnotationDbi keys from one column to another. |
| mean_by_bioreplicate | An attempt to address a troubling question when working with... |
| mean_by_factor | Runs median_by_factor with fun set to 'mean'. |
| median_by_factor | Create a data frame of the medians of rows by a given factor... |
| mesg | message() but with a verbose flag. |
| model_test | Make sure a given experimental factor and design will play... |
| my_identifyAUBlocks | copy/paste the function from SeqTools and figure out where it... |
| my_isva | There are some funky scoping problems in isva::DoISVA(). |
| mymakeContrasts | A copy of limma::makeContrasts() with special sauce. |
| myretrieveKGML | A couple functions from KEGGgraph that have broken |
| my_runsims | A version of PROPER:::runsims which is (hopefully) a little... |
| network_from_matrix | Given a matrix of scores (bit score, e-value, etc), create an... |
| noiseq_pairwise | Perform pairwise comparisons using noiseq. |
| normalize | Simplified and ideally improved normalization function |
| normalize_counts | Perform a simple normalization of a count table. |
| normalize_expt | Normalize the data of an expt object. Save the original... |
| normalize_se | Normalize a SummarizedExperiment and think about how I want... |
| notes-expt-method | A getter to pull the notes an expt. |
| orgdb_from_ah | Get an orgdb from an AnnotationHub taxonID. |
| overlap_geneids | Mostly as a reminder of how to get the gene IDs from a... |
| overlap_groups | Extract overlapping groups from an upset |
| parse_msigdb | Parse either xml or sqlite data from MSigDB. I think I will... |
| parse_msigdb_sqlite | Extract metadata from the msigdb sqlite data. |
| parse_msigdb_xml | Extract fun experimental metadata from a MSigDB xml file. |
| pattern_count_genome | Find how many times a given pattern occurs in every gene of a... |
| pca_highscores | Get the highest/lowest scoring genes for every principle... |
| pca_information | Gather information about principle components. |
| pct_all_kegg | Extract the percent differentially expressed genes for all... |
| pct_kegg_diff | Extract the percent differentially expressed genes in a given... |
| pData-expt-method | A getter to pull the experimental metadata from an expt. |
| pData-set-expt-ANY-method | A setter to put the experimental metadata into an expt. |
| pData-set-SummarizedExperiment-ANY-method | A setter to put the experimental metadata into a... |
| pData-SummarizedExperiment-method | A getter to pull the experimental metadata from a... |
| pipe | Pipe operator |
| please_install | Automatic loading and/or installing of packages. |
| plot_3d_pca | Something silly for Najib. |
| plot_batchsv | Make a dotplot of known batches vs. SVs. |
| plot_bcv | Steal edgeR's plotBCV() and make it a ggplot2. |
| plot_boxplot | Make a ggplot boxplot of a set of samples. |
| plot_cleaved | Plot the average mass and expected intensity of a set of... |
| plot_corheat | Make a heatmap.3 description of the correlation between... |
| plot_density | Create a density plot, showing the distribution of each... |
| plot_de_pvals | Given a DE table with p-values, plot them. |
| plot_disheat | Make a heatmap.3 of the distances (euclidean by default)... |
| plot_dist_scatter | Make a scatter plot between two sets of numbers with a cheesy... |
| plot_enrichresult | Invoke ther various fun plots created by Guangchuang Yu. |
| plot_epitrochoid | Make epitrochoid plots! |
| plot_essentiality | Plot the essentiality of a library as per DeJesus et al. |
| plot_fun_venn | A quick wrapper around venneuler to help label stuff |
| plot_goseq_pval | Make a pvalue plot from goseq data. |
| plot_gostats_pval | Make a pvalue plot similar to that from clusterprofiler from... |
| plot_gprofiler2_pval | Make a pvalue plot from gprofiler data. |
| plot_gprofiler_pval | Make a pvalue plot from gprofiler data. |
| plot_heatmap | Make a heatmap.3 plot, does the work for plot_disheat and... |
| plot_heatmap-data.frame-method | Run plot_heatmap with a dataframe as input. |
| plot_heatmap-ExpressionSet-method | Run plot_heatmap with an ExpressionSet as input. |
| plot_heatmap-expt-method | Run plot_heatmap with an expt as input. |
| plot_heatmap-SummarizedExperiment-method | Run plot_heatmap with a SummarizedExperiment as input. |
| plot_heatplus | Potential replacement for heatmap.2 based plots. |
| plot_histogram | Make a pretty histogram of something. |
| plot_hypotrochoid | Make hypotrochoid plots! |
| plot_intensity_mz | Plot mzXML peak intensities with respect to m/z. |
| plot_legend | Scab the legend from a PCA plot and print it alone |
| plot_libsize | Make a ggplot graph of library sizes. |
| plot_libsize-data.frame-factor-character-method | Run plot_libsize() with a dataframe as input. |
| plot_libsize-ExpressionSet-ANY-ANY-method | Run plot_libsize() with an ExpressionSet as input. |
| plot_libsize-expt-ANY-ANY-method | Run plot_libsize() with an expt as input. |
| plot_libsize_prepost | Visualize genes observed before/after filtering. |
| plot_libsize-SummarizedExperiment-ANY-ANY-method | Send a SummarizedExperiment to plot_libsize(). |
| plot_linear_scatter | Make a scatter plot between two groups with a linear model... |
| plot_ly | Plotly for interactive 3-D plotting in the Shiny App |
| plotly_pca | Plot a PC plot with options suitable for ggplotly. |
| plot_ma_condition_de | Create a MA plot with colors from the original expressionset. |
| plot_ma_de | Make a pretty MA plot from one of limma, deseq, edger, or... |
| plot_metadata_factors | Produce plots of metadata factor(s) of interest. |
| plot_meta_sankey | Plot metadata factors as a sankey diagram. |
| plot_meta_sankey-expt-method | Feed an expt to a sankey plot. |
| plot_multihistogram | Make a pretty histogram of multiple datasets. |
| plot_multiplot | Make a grid of plots. |
| plot_mzxml_boxplot | Make a boxplot out of some of the various data available in... |
| plot_nonzero | Make a ggplot graph of the number of non-zero genes by... |
| plot_nonzero-ExpressionSet-method | Make a nonzero plot given an ExpressionSet |
| plot_nonzero-expt-method | Make a nonzero plot given an expt. |
| plot_nonzero-SummarizedExperiment-method | Make a nonzero plot given a SummarizedExperiment |
| plot_num_siggenes | Given a DE table with fold changes and p-values, show how... |
| plot_ontpval | Make a pvalue plot from a df of IDs, scores, and p-values. |
| plot_pairwise_ma | Plot all pairwise MA plots in an experiment. |
| plot_pca | Make a PCA plot describing the samples' clustering. |
| plot_pca_genes | Make a PC plot describing the gene' clustering. |
| plot_pcfactor | make a dotplot of some categorised factors and a set of... |
| plot_pcload | Print a plot of the top-n most PC loaded genes. |
| plot_pcs | Plot principle components and make them pretty. |
| plot_pct_kept | Make a ggplot graph of the percentage/number of reads... |
| plot_peprophet_data | Plot some data from the result of extract_peprophet_data() |
| plot_pyprophet_counts | Count some aspect(s) of the pyprophet data and plot them. |
| plot_pyprophet_distribution | Make a boxplot out of some of the various data available in... |
| plot_pyprophet_points | Plot some data from the result of extract_pyprophet_data() |
| plot_pyprophet_protein | Read data from pyprophet and plot columns from it. |
| plot_pyprophet_xy | Invoked plot_pyprophet_counts() twice, once for the x-axis,... |
| plot_qq_all | Quantile/quantile comparison of the mean of all samples vs.... |
| plot_rmats | Given some psi and tpm data from rMATS, make a pretty plot! |
| plot_rpm | Make relatively pretty bar plots of coverage in a genome. |
| plot_sample_bars | The actual library size plotter. |
| plot_sample_cvheatmap | An experiment to see if I can visualize the genes with the... |
| plot_sample_heatmap | Make a heatmap.3 description of the similarity of the genes... |
| plot_sample_heatmap-ExpressionSet-method | Plot a sample heatmap of an ExpressionSet. |
| plot_sample_heatmap-expt-method | Plot the sample heatmap of an expt. |
| plot_sample_heatmap-SummarizedExperiment-method | Plot a sample heatmap with a SummarizedExperiment. |
| plot_sankey_de | Make a sankey plot showing how the number of genes deemed... |
| plot_scatter | Make a pretty scatter plot between two sets of numbers. |
| plot_seurat_scatter | Make a few of the likely scatterplots provided by... |
| plot_significant_bar | Plot significant genes by contrast with different colors for... |
| plot_single_qq | Perform a qqplot between two columns of a matrix. |
| plot_sm | Make an R plot of the standard median correlation or distance... |
| plot_sm-data.frame-method | Plot the standard median pairwise values of a dataframe. |
| plot_sm-ExpressionSet-method | Plot the standard median pairwise values of an ExpressionSet. |
| plot_sm-expt-method | Plot the standard median pairwise values of an expt. |
| plot_sm-SummarizedExperiment-method | Plot the standard median pairwise values of a... |
| plot_spirograph | Make spirographs! |
| plot_suppa | Given some psi and tpm data, make a pretty plot! |
| plot_svfactor | Make a dotplot of some categorised factors and a set of SVs... |
| plot_topgo_densities | Plot the density of categories vs. the possibilities of all... |
| plot_topgo_pval | Make a pvalue plot from topgo data. |
| plot_topn | Plot the representation of the top-n genes in the total... |
| plot_tsne | Shortcut to plot_pca(pc_method = "tsne") |
| plot_variance_coefficients | Look at the (biological)coefficient of variation/quartile... |
| plot_variance_coefficients-ExpressionSet-method | Plot the coefficient of variance values of an ExpressionSet. |
| plot_variance_coefficients-expt-method | Plot the coefficient of variance values of a... |
| plot_variance_coefficients-SummarizedExperiment-method | Plot the coefficient of variance values of a... |
| plot_volcano_condition_de | Theresa's volcano plots are objectively nicer because they... |
| plot_volcano_de | Make a pretty Volcano plot! |
| pp | Plot a picture, with hopefully useful options for most(any)... |
| primer_qc | Perform a series of tests of a putative primer. |
| print.abundant_genes | Print a summary of a set of abundant genes. |
| print.all_gprofiler | Print the result of all_gprofiler() |
| print.all_pairwise | Print function for a pairwise differential expression result. |
| print.annotations_biomart | Print function for a set of annotations downloaded from... |
| print.aucc_info | Print the result from calculate_aucc(). |
| print.biomart_go | Print the results of load_biomart_go(). |
| print.cds_variant_primers | Print the results of snp_cds_primers(). |
| print.classified_mutations | Print the results of classify_snps(). |
| print.classifier_evaluation | Print the result from self_evaluate_model(). |
| print.clusterprofiler_result | Print a clusterprofiler over representation search. |
| print.combined_de | Print a combined differential expression analysis. |
| print.combined_table | Print a single combined DE result. |
| print.correlation_heatmap | Print the result of plot_corheat(). |
| print.cross_table_comparison | Print a representation of compare_de_tables(). Note I think I... |
| print.density_plot | Print the result from plot_density(). |
| print.density_primers | Print a summary of putative PCR primers based on variant... |
| print.deseq_lrt | Print the result of running deseq_lrt(). |
| print.distance_heatmap | Print the result of plot_disheat(). |
| print.expt | Modified print function for an expt. |
| print.goseq_result | Print a goseq over representation search. |
| print.gostats_result | Print a gostats over representation search. |
| print.gprofiler_result | Print a gprofiler over representation search. |
| print.graphed_metrics | Print a message about the results from graph_metrics(). |
| print.gsva_result | Print a gsva category search. |
| print.gsva_sig | Print gsva categories deemed 'significant'. |
| print.legend_plot | Print a legend of an expressionset. |
| print.libsize_plot | Print the library sizes from an experiment. |
| print.mapped_keepers | Print a set of mapped keepers from combine_de_tables() |
| print.meta_sankey | Print a metadata sankey plot. |
| print.nonzero_plot | Print a nonzero plot. |
| print.partitioned_data | Print something useful about the result of... |
| print.pattern_counted | Print some information about a pattern counted genome |
| print.pca_result | Print the result from one of the various dimension... |
| print.prepost_filter | Print a representation of the pre vs. post filtered data. |
| print.preprocessing_metadata | Print the result from gather_preprocessing_metadata(). |
| print.proper_estimate | Print the result from simple_proper(). |
| print.reordered_varpart | Print the result of a reordered variance partition analysis. |
| print.sig_genes | Print some significantly differentially expressed genes. |
| print.sig_intersect | Print the intersection of significant genes from multiple... |
| print.snp_intersections | Print some information about the result of... |
| print.snp_sets | Print the result of get_snp_sets(). |
| print.snps_genes | Print the result of snps_vs_genes(). |
| print.standardmedian_plot | Print the result of plot_sm() |
| print.topgo_result | Print a topgo over representation search. |
| print.topn_plot | Print a result from plot_topn(). |
| print_ups_downs | Reprint the output from extract_significant_genes(). |
| print.varcoef_plot | Print a result from plot_variance_coefficients(). |
| print.varpart | Print variance partition results. |
| print.written_expt | Print the result from write_expt. |
| print.written_xlsx | Print the result from write_xlsx. |
| proportions_by_factors | Extract the proportions of each group/sample in a scd. |
| prune_network | Exclude nodes from a network which are not well connected. |
| pull_git_commit | Reset the chosen git repository to a chosen commit. |
| random_ontology | Perform a simple_ontology() on some random data. |
| rank_order_scatter | Plot the rank order of the data in two tables against each... |
| rbind_summary_rows | Append rows containing summary() information. |
| read_counts_expt | Read a bunch of count tables and create a usable data frame... |
| read_metadata | Given a table of meta data, read it in for use by... |
| read_snp_columns | Read the output from bcfutils into a count-table-esque |
| read_thermo_xlsx | Parse the difficult thermo fisher xlsx file. |
| recolor_points | Quick point-recolorizer given an existing plot, df, list of... |
| record_seurat_samples | Add into the miscellaneous SCD slot a dataframe with some... |
| renderme | Add a little logic to rmarkdown::render to date the final... |
| replot_varpart_percent | A shortcut for replotting the percent plots from... |
| rex | Send the R plotter to the computer of your choice! |
| rowData-ExpressionSet-method | A getter of the gene information from an ExpressionSet,... |
| rowData-expt-method | A getter of the gene information from an expt, synonymous... |
| rowData-set-expt-method | A setter to put the gene information into an expt. |
| rowmax_filter_counts | Filter low-count genes from a data set only using a simple... |
| rowMeans | Make sure BiocGenerics' version of rowMeans is available. |
| s2s_all_filters | Gather together the various SWATH2stats filters into one... |
| sampleNames-expt-method | A getter to get the samples names from an expt. |
| sampleNames-set-expt-ANY-method | A setter to put the samples names into an expt. |
| sampleNames-set-SummarizedExperiment-ANY-method | A setter to put the samples names into a... |
| sampleNames-SummarizedExperiment-method | A getter to get the samples names from a... |
| sanitize_expt | Get rid of characters which will mess up contrast making and... |
| sanitize_expt_fData | Given an expressionset, sanitize the gene information data. |
| sanitize_expt_pData | Adding an alias to sanitize_metadata until I decide how I... |
| sanitize_metadata | Given an expressionset, sanitize pData columns of interest. |
| sanitize_number_encoding | Re-encode South American numbers so they fit my... |
| sanitize_percent | Sanitize unreliable presentation of percent values from... |
| saveme | Make a backup rdata file for future reference |
| score_gsva_likelihoods | Score the results from simple_gsva(). |
| score_mhess | A scoring function for the mh_ess TNSeq method. |
| self_evaluate_model | Create a confusion matrix and ROC of a model against its... |
| semantic_copynumber_extract | Extract multicopy genes from up/down gene expression lists. |
| semantic_copynumber_filter | Remove multicopy genes from up/down gene expression lists. |
| semantic_expt_filter | Remove/keep specifically named genes from an expt. |
| sequence_attributes | Gather some simple sequence attributes. |
| sequential_variants | Search a set of variants for ones which are relatively... |
| set_expt_batches | Change the batches of an expt. |
| set_expt_colors | Change the colors of an expt |
| set_expt_conditions | Change the condition of an expt |
| set_expt_factors | Change the factors (condition and batch) of an expt |
| set_expt_genename_column | Switch the gene names of an expressionset using a column from... |
| set_expt_genenames | Change the gene names of an expt. |
| set_expt_samplenames | Change the sample names of an expt. |
| shiny | Shiny App for interactively visualizing RNAseq data |
| significant_barplots | Given the set of significant genes from combine_de_tables(),... |
| sig_ontologies | Take the result from extract_significant_genes() and perform... |
| sillydist | Calculate a simplistic distance function of a point against... |
| simple_clusterprofiler | Perform the array of analyses in the 2016-04 version of... |
| simple_cp_enricher | Generic enrichment using clusterProfiler. |
| simple_dorothea | Invoke dorothea in an attempt to hunt down cool TFs. |
| simple_filter_counts | Filter low-count genes from a data set only using a simple... |
| simple_gadem | run the rGADEM suite |
| simple_goseq | Perform a simplified goseq analysis. |
| simple_gostats | Simplification function for gostats, in the same vein as... |
| simple_gprofiler | Redirect users to simple_gprofiler2 |
| simple_gprofiler2 | Run searches against the web service g:Profiler. |
| simple_gprofiler_old | Run searches against the web service g:Profiler. |
| simple_gsva | Provide some defaults and guidance when attempting to use... |
| simple_motifRG | Run motifRG on a fasta file. |
| simple_pathview | Print some data onto KEGG pathways. |
| simple_proper | Invoke PROPER and replace its default data set with data of... |
| simple_topgo | Perform a simplified topgo analysis. |
| simple_topgo-character-method | Coerce simple_topgo to accept a vector of gene IDs instead of... |
| simple_varpart | Use variancePartition to try and understand where the... |
| simple_xcell | Invoke xCell and pretty-ify the result. |
| single_topgo_tree | Collapse the logic for collecting topgo trees into one little... |
| skim_seurat_metadata | Use skimr to make pretty summaries of cell-data. |
| slide_de_threshold | make a slideable threshold for cutting off significant genes... |
| sm | Silence |
| snp_by_chr | The real worker. This extracts positions for a single... |
| snp_cds_primers | Look for variants associated with CDS regions instead of... |
| snp_density_primers | Create a density function given a variant output and some... |
| snpnames2gr | Take a vector of my peculiarly named variants and turn them... |
| snps_intersections | Cross reference observed variants against the transcriptome... |
| snp_subset_genes | Look for only the variant positions in a subset of genes. |
| snps_vs_genes | Make a summary of the observed snps by gene ID. |
| snps_vs_genes_padded | A copy of the above function with padding for species without... |
| state | Get the state of the data in an expt. |
| state-expt-method | Extract the state of an expt vis a vis normalization. |
| state-set | Set the state of the data in an expt. |
| state-set-expt-method | Put the current state into an expt. |
| state-set-SummarizedExperiment-method | Put the state into a SummarizedExperiment. |
| state-SummarizedExperiment-method | Get the state from a SummarizedExperiment. |
| steal_salmon_tx_ids | Steal transcript IDs from the first count table. |
| sub-.expt | Subset an expt |
| subset_expt | Extract a subset of samples following some rule(s) from an... |
| subset_expt-SummarizedExperiment-method | Subset a SummarizedExperiment with some extra syntax. |
| subset_genes | Exclude some genes given a pattern match |
| subset_ontology_search | Perform ontology searches on up/down subsets of differential... |
| sub-sub-expt-character-ANY-method | Simplifying subset on metadata. |
| subtract_expt | Try a very literal subtraction |
| sum_eupath_exon_counts | I want an easy way to sum counts in eupathdb-derived data... |
| sum_exon_widths | Given a data frame of exon counts and annotation information,... |
| summarize_scd_clusters | Summarize scores across observed clusters in a scd. |
| summarize_ups_downs | Create a summary table of the ranges of fold-change values of... |
| sva_modify_pvalues | Use sva's f.pvalue to adjust p-values for data adjusted by... |
| synchronize_expt | Synchronize the extra elements of an expt with a new... |
| table_style | Set the xlsx table style |
| tar_meta_column | Make an archive using a column from the metadata. |
| tempfile | A cheater redefinition of tempfile. |
| tmpmd5file | A hopefully more robust version of tempfile(). |
| tnseq_multi_saturation | Plot the saturation of multiple libraries simultaneously. |
| tnseq_saturation | Make a plot and some simple numbers about tnseq saturation |
| topDiffGenes | A very simple selector of strong scoring genes (by p-value) |
| topgo2enrich | Convert a simple_topgo() result to an enrichResult. |
| topgo_tables | Make pretty tables out of topGO data |
| topgo_trees | Print trees from topGO. |
| transform_counts | Perform a simple transformation of a count table (log2) |
| unAsIs | Remove the AsIs attribute from some data structure. |
| u_plot | Plot the rank order svd$u elements to get a view of how much... |
| upsetr_combined_de | Make an upset plot of all up/down genes in a set of... |
| upsetr_sig | Use UpSetR to compare significant gene lists. |
| variance_expt | Add some gene annotations based on the mean/variance in the... |
| varpart_summaries | Attempt to use variancePartition's fitVarPartModel()... |
| verbose | Set a default verbosity, for now this just queries if this is... |
| wgcna_network | Just putting down an example from Alejandro's work and... |
| what_happened | Print a string describing what happened to this data. |
| write_basic | Writes out the results of a basic search using... |
| write_cds_entries | Extract CDS sequences from a genome and set of annotations. |
| write_classifier_summary | Write out the results of classify_n_times(). |
| write_combined_legend | Write the legend of an excel file for combine_de_tables() |
| write_combined_summary | Internal function to write a summary of some combined data |
| write_cp_data | Make a pretty table of clusterprofiler data in excel. |
| write_density_primers | Write out a set of primers for testing. |
| write_deseq | Writes out the results of a deseq search using... |
| write_de_table | Writes out the results of a single pairwise comparison. |
| write_edger | Writes out the results of a edger search using... |
| write_expt | Make pretty xlsx files of count data. |
| write_goseq_data | Make a pretty table of goseq data in excel. |
| write_gostats_data | Make a pretty table of gostats data in excel. |
| write_go_xls | Write gene ontology tables for excel |
| write_gprofiler_data | Write some excel results from a gprofiler search. |
| write_gsva | Write out my various attempts at making sense of gsva. |
| write_limma | Writes out the results of a limma search using... |
| write_sample_design | Put the metadata at the end of combined_de_tables() |
| write_sig_legend | Internal function to write a legend for significant gene... |
| write_snps | Write a matrix of variants in an alignment-esque format. |
| write_subset_ontologies | Write gene ontology tables for data subsets |
| write_suppa_table | Take a set of results from suppa and attempt to write it to a... |
| write_topgo_data | Make a pretty table of topgo data in excel. |
| write_xlsx | Write a dataframe to an excel spreadsheet sheet. |
| write_xlsx-ANY-ANY-ANY-written_xlsx-method | Write an xlsx file given the result of an existing xlsx... |
| xlsx_insert_png | An attempt to improve the behaivor of openxlsx's plot... |
| xref_regions | If I were smart I would use an I/GRanges for this. |
| ymxb_print | Print a model as y = mx + b just like in grade school! |
