| add.qual.att | Add a (named) column to a data.frame, filled with the same... |
| barplotCommonGenesUnique2D | Plot the genes in common between 2 datasets |
| barplotCommonGenesUnique3D | Plot the genes in common between 3 datasets |
| bibarplotsDiversityCond | For easier comparison, plot the uniquely expressed genes... |
| bluered | Generate blue-to-red colorscale |
| boolDF2numeric | Convert a logical data.frame to a numeric data.frame (TRUE ->... |
| cat.html | Encapsulate result between <pre></pre> html tags |
| change.localID | Change the name of the samples based on preset annotation... |
| checkConformity | Check that both datasets share identical dimensions |
| clean.HTSc | Remove rows from data.frame (created by older version of... |
| clean.infinite | Replace one value by another and remove all NA rows |
| cleanNames | Take a character string with parenthensis as a pattern and... |
| cleanReadAnnot | Allows to load an annotation data.frame |
| cleantable | Wrapper around knitr::kable with HTML as a default |
| colCbc | Wrapper around colorRampalette with two prechosen colours. |
| colMax | Gives the maximum value of each column |
| colMin | Gives the minimum value of each column |
| colorpanel | Generate a smoothly varying set of colors |
| colSelect | Selection on a data.frame to keep or filter out specified... |
| colSelect2 | Selection on a data.frame to keep the specified columns only |
| comp_cor_log2 | Compute the correlation between two studies after their... |
| complement2nbGenesPerCond.unique | Facetted plot (e.g. per study) of the distribution of genes... |
| completeDF.t_test.CorrMat_identical.vs.different | Apply t.test.CorrMat_identical.vs.different and complete the... |
| comp_ratio_sd | Calculate the ratio of standard deviation between two... |
| computeBreadth | Compute breadth of expression of the genes across a... |
| compute_gene_cor | Compute for the genes the correlation of their expression... |
| compute_gene_cor_save | Allows to save to a file the correlation of the genes... |
| compute_permuted_cor | Shuffle randomly one expression dataset before computing the... |
| compute_permuted_corQ | Optimised to work with clustermq (to be used for LSF jobs)... |
| compute_tissue_corr_matrix | Compute the correlation between two matrices variables(... |
| createDFhXg | Allow to select one tissue only from a data.frame |
| createGoAnnot | Retrieve GO information for a list of genes or all genes |
| createTableResults_basics | Format results output for two-dataframe meta-analysis |
| creationDf.gxa | Wrapper around read.table with a few tweaks |
| cross.select | Keep only the columns or rows or both that are common between... |
| cross.selectCond | Selection of the same conditions (columns) between two... |
| cross.sharedDistrib | Compute and compare the breath of expression of two studies... |
| cross.sharedDistrib_firstLast | Draw the figures of the shared expression for the two... |
| crudeStrip | Strip rows which don't have any value above the given... |
| Cumulative_spe | Rank the genes based on their decreasing order of correlation... |
| cumulSpe | Allows to plot the amount of TS genes among the genes that... |
| cumulSpeSimulAggregated | Plot the course of TS proteins when the level of genes... |
| cutoff | Test cell values in a data.frame for equality or higher value... |
| dataset.HTSc | Create a data.frame from a folder of htseq outputs |
| dataset_irap | Create a data.frame for a transcriptomic study from the... |
| dataset.randomize | Randomise the content of each column of a data.frame |
| datatable.custom | Create a customised HTML table widget based on the DT library |
| density_plot | Wrapper around gpplot2's density plot with preset arguments |
| df.cutoff | Create a data.frame for which the values under a given... |
| df.cutoff2 | Create a data.frame for which the values under a given... |
| df.fill | Create a data.frame with new rows or columns for the inputed... |
| df.Strip | Filter the content of a numeric data.frame based on a... |
| df.StripLine | Compare cell values to a threshold and fill cells that failed... |
| drawOverlapHeatmaps | Draw the heatmap based on the output of matrix overlap_res |
| DrawVenn | Function based on the VennDiagram package with some... |
| ebiRank | Rank expression of the genes within each tissue. |
| enhancedTissue | Give the list of the genes whose expression is enhanced for a... |
| enrichedTissue | Give the list of the genes whose expression is enriched for a... |
| evolCorrCumul | Plot the correlation of the gene expression between the same... |
| evolCvCorrCumul | Plot the correlation of the gene expression while taking in... |
| excludeGenes | Exclude the genes (rows) from a data.frame based on a given... |
| excludeRows | Create a data.frame for which specific rows have been... |
| ExpressedGeneInTissue | Returns the id (rownames) of the genes that are found in the... |
| extractDendroFromPlotTD | Extract the dendrogram from the heatmap based on... |
| extractDendroTissueDistance | Create a dendrogram from a tissueDistance data.frame |
| extract.HTSc | Allows to format older version of irap's output |
| extract.irap | Import data from files produced by an older version of irap. |
| extractSpe | Extract the genes that are specific to a tissue |
| extractWithinSampleAbundance | Extract columns that contains "WithInSampleAbundance." in... |
| extractWithinSampleTop3Abundance | Extract columns that contains "WithInSampleTop3Abundance." in... |
| extractWithTag | Allows to create a function that extracts the columns that... |
| factorDF2string | Convert all the content of a given data.frame to characters |
| factoring | From a list of filenames, return a list of data.frames after... |
| factoring.rbind | From a list of data.frame, add an attribute and collate (row... |
| filtre.dataset | Keep only the specified rows of a dataframe |
| fixNamesGtex | Homogenise the names of the GTEx data with the other datasets... |
| fixNamesUhlen | Homogenise the names of the Uhlen et al. data with the other... |
| gen.add.qual.att | Create a function that allows to add a qualitative attribute... |
| geneClassify | Classify the genes in function of their expression. Inspired... |
| geneClassify.Q | Classify the genes in function of their expression to be used... |
| geneScatters | Scatter plot for the expression of a gene for two datasets... |
| getEpsilon | Displays the value of epsilon |
| gg_color_hue | Create a palette with ggplot2 default colors |
| g_legend | Extract the legend from a ggplot |
| go2genes | Takes a list of GO ids and queries all the genes related to... |
| grapes-greater-than-equals-grapes | Test more carefully if x is equal or greater than y |
| grapes-less-than-equals-grapes | Test more carefully if x is equal or lesser than y |
| greenred | Generate green-to-red colorscale |
| hampel.test | Apply an Hampel's test on a data.frame |
| heatmap.2 | Enhanced Heat Map (from gplots) |
| heatmapAlpabet | Draw a customised heatmap where the different variables are... |
| heatmapAlphabet | Draw a customised heatmap where the different variables are... |
| heatmapWithClustering | Draw a customised heatmap with marked clusters in the margins... |
| initialise | barzinePhdR |
| internalJaccardIndMatrix | Create matrix of jaccard indices based on the output of... |
| Intersect | Allow to intersect more than two sets at a time |
| jaccardInd | Compute Jaccard index |
| lg.format | Format a data.frame in long format and annotate columns |
| List | Save the output of "[<-.result" function |
| listFromFile | Create a vector from a file where the data is formatted as a... |
| listFromFileBiomart | Create a vector from a file downloaded from Biomart where the... |
| listgenes | Retrieve all the genes ID from a file |
| ListOfExpressedGenes | Give the list of expressed genes in a study in function of... |
| Load | Load function that returns the object(s) instead of attaching... |
| load_and_check_3DF | Load three data.frames from file paths and check that they... |
| log2.na | The correct answer -Inf for log2(0) is changed to NA |
| make.2ldf | Create a data.frame from the elements of two vectors that... |
| make.3ldf | Create a data.frame from the elements of three vectors that... |
| matchColCond | Allows to display the correct colour annotation |
| matrix.overlap_res | Calculate the overlap of specific genes (uniquely expressed... |
| maxCond.df | Give the maximum value observed for each gene across all... |
| merge_biol_rep | Merge the biological replicates in a data.frame together |
| merge_replicates | Merge the replicates of a data.frame together |
| merge_tech_rep | Merge the techincal replicates in a data.frame together |
| mHeatmap | Wrapper around heatmap.2; allows to annotate with the colours... |
| mHeatmapTC | Wrapper around heatmap.2; allows to annotate with the colours... |
| mixed.high | Provide the list of mixed high genes |
| mixed.high2 | Provide the list of genes that have a high expression when... |
| mixed.low | Provide the list of mixed low genes |
| mixed.low2 | Provide the list of genes that have a low expression when... |
| mkMatrix | Take two data.frames to create one and can log2 the content... |
| multi.add.qual.att | Create a dataframe filled with a value with the same number... |
| multibarplotsDiversityCond | For easier comparison, plot the uniquely expressed genes... |
| nameID | Retrieve gene symbols (hgnc) for Ensembl gene IDs with... |
| NAto0 | Convert all missing values to 0 |
| nbGenesPerCond | Present the number of genes that are expressed in each tissue |
| nbGenesPerCond.unique | Plot the distribution of genes across the columns. Genes... |
| nl1d | Creates a two-column data.frame from a named vector where the... |
| noMoreFactor | Change all factor columns in a data.frame into character... |
| overlapProtTrans.Specific | Compute test of significance and draw venn diagram of the... |
| overlapSortCumul2DF | Give the number of the common genes between two datasets at... |
| overlapSortCumul5DF | Give the number of the common genes between five datasets at... |
| overlapSpeProtmRNA | Overlap of the tissue-specific proteins with the most... |
| plot_distribDF | Plot the distribution for the columns of a data.frame... |
| plotGOHeatmap | Create a heatmap from a compareClusterResult... |
| plotTissuesDistance | Plot heatmap based on the result of tissueDistance |
| plotUniq.distrib | More customisable plot based on computeBreadth |
| plot_xsharedDistrib | Plot the expression breadth distribution computed with... |
| prefix | Prefix the names of the columns of a data.frame with a tag |
| prefixv | Prefix character vector with a given tag |
| presentData | Wrapper that briefly present the datasets |
| printDebug | For debugging purposes Screen or report output Look for a... |
| protSpe | Give the list of rows for which the values are only once... |
| qLoad | Load in the working environment the object matching the name... |
| rank.Atlas | Rank for each tissue (column) the genes (rows) based on their... |
| rankSpe | Rank gene expression based on their specificity to each... |
| ratioSpe | Compute the tissue specificity of the genes to each tissue as... |
| ratioSpe.1 | Give the gene specificity in each tissue as a ratio to its... |
| read.list | Read a file (one or two columns) and creates a vector (named... |
| Read.table | Basically a read.table but with predetermnined parameters |
| redblue | Generate red-to-blue colorscale |
| redgreen | Generate red-to-green colorscale |
| refGraphDF | Create a data.frame from the two data.frames after filtering... |
| relative.GXenrichement | Annotate the genes that the expression is enriched of... |
| relative.GXenrichement2 | Another function that annotate the genes that the expression... |
| relnum.GXenrichement | Another function that annotates the genes that the expression... |
| removeClusters | Remove the proteins that are part of a cluster |
| replotCumulSpeSimulAggregated | Plot a figure based on the data.frame created by the... |
| revCustom | Reverse a data.frame (or matrix) and change '-Inf' in 'NA' or... |
| revCustomMatrixDist | Reverse a symetric data.frame (or matrix). Specifically... |
| rowCV | Covariance applied to a data.frame rows |
| RowMad | Median absolute deviation applied to a data.frame rows |
| rowMax | Gives the maximum value of each row |
| RowMeans | Arithmetical mean applied to a data.frame rows |
| RowMedians | Arithmetical median applied to a data.frame rows |
| rowMin | Gives the minimum value of each row |
| RowMode | Mode applied to a data.frame rows |
| rowSD | Standard deviation applied to a data.frame rows |
| rowVar | Variance applied to a data.frame rows |
| rpkm2tpm | Convert R/FPKM to TPM |
| save_df | Allow to save a data.frame quicly. |
| saveToFile | Takes an object and saves it in a file with the same name.... |
| saveWithName | Allows changing the name of the object at the same time that... |
| scatplot | Scatter plot of two columns of a data.frame after possible... |
| scatplot.log2 | Scatter plot of two columns of a data.frame after log2... |
| selectSpecific | Select specifically the genes that are expressed above a... |
| setDebug | Allow to change the value of debug |
| setEpsilon | Allows to change the value of epsilon (needed to circumvent... |
| sharedBreadth | Plot the breadth of a first study compared to a second one. |
| signifDF | Round numbers to the specified number of significant digits... |
| simpleCap | Capitalise the first character of a string |
| simpleCap2 | Capitalise the first character of a string |
| single.factoring | From a file outputted by an older version of irap, create a... |
| single.factoring2 | From a filename, extract a data.frame to which a number of... |
| sortedGenesCorr | Plot the correlation of different studies comparison that are... |
| sortUhlenClassInOne | Create one data.frame with the most relevant information for... |
| stamped | Attach the current time to a string name |
| stat.mode | Statistical mode value |
| strip | Strip the rows of a data.frame that are failling the test. |
| subset-.result | Allows to output a list directly in several objects (python... |
| substrRight | Extract the last n character(s) from a string |
| suffix | Tag each column name of a data.frame with a given string of... |
| tableGeneIDdesc | Retrieve additional gene information from biomaRt |
| test_CorrMat_identical_different | Create the data.frame and can also test and plot the... |
| theme_cbw | Theme black and white with centered title |
| theme_legacy | Theme Legacy theme grey |
| theme_minimaliste | Theme minimaliste: customised theme for ggplot2 |
| tissuesDistance | Compute the distance between the tissues within a study. |
| topCommonGenes | Gives the number or the refenrences of shared genes by both... |
| topgenes.corCluster | Compute the correlation matrix for the correlation of the two... |
| topgenes.corClusterDraw | Draw (after computation) the correlation matrix for the... |
| topgenes.corClusterDraw_log | Draw (after computation) the correlation matrix for the... |
| topgenes.corCluster_log | Compute the correlation matrix for the correlation of the two... |
| trimSpace | Remove empty spaces in strings |
| t_test.CorrMat_identical.vs.different | Test with a Welch t-test between the group of similar tissues... |
| t_test.Mat_identical.vs.different | Test with a Welch t-test between the group of similar tissues... |
| ubi.high | Give the genes (rows) that are ubiquitously highly expressed... |
| ubi.low | Give the genes (rows) that are ubiquitously lowly expressed... |
| ubi.strict | Give the names of all the genes (rows) that are strictly... |
| undetected | List all the genes (rows) for which no expression was... |
| Union | Allow to intersect more than two sets at a time |
| unmatchedRowsAbyB | Rows that are unmatched in one dataset by any row in another... |
| unmatchedRowsAbyBC | Rows that are unmatched in one dataset by any row in two... |
| usablePath | Check if path is available for write |
| vennPlot_spe | Compare the content of the two first columns of a data.frame... |
| wrap.compute_permuted_corQ_save | Wrapper to run the random shuffling of the gene correlation... |
| wrap.scatplot.log2 | Wrapper automating the creation of scatter plots... |
| wtDF | write.table applied to DF plus some general customisation |
| xsharedDistrib | Compute and compare the breadth of expression of two datasets... |
