A B C D E F G H K L M N O P R S T U W X misc
| addBeforFileExtension | Add text before file-extension | 
| adjBy2ptReg | Linear rescaling of numeric vertor or matrix | 
| adjustUnitPrefix | Adjust Value With Different Decimal Prefixes To Single Prefix Plus Unit | 
| appendNR | Append vectors or lists, without duplcating common elements | 
| arrayCV | CV of array | 
| asSepList | Organize Data as Separate List-Entries | 
| buildTree | Connect edges to from tree and extract all possible branches | 
| cbindNR | cbind to non-redundant | 
| checkAvSd | Check how multiple groups of data separate or overlap based on mean +/- sd | 
| checkFilePath | Verify File-name If Existing (in specified path), If Has Proper Extension Or Select Files With Proper Extension From Given Path | 
| checkGrpOrder | checkGrpOrder | 
| checkGrpOrderSEM | Check order of multiple groups including non-overlapping SEM-margins | 
| checkSimValueInSer | Check for similar values in series | 
| checkStrictOrder | Check for strict (ascencing or descending) order | 
| checkUnitPrefix | Check For Common Unit-Name in Text | 
| checkVectLength | Check length of vector | 
| cleanReplicates | Replace Most Distant Values by NA | 
| closeMatchMatrix | Reorganize results of search for close (similar) values in matrix-view | 
| coinPermTest | Compare Means Of Two Vectors By Permutation Test | 
| colCVs | rowCVs | 
| colMedSds | Standard Error Of Median For Each Column By Bootstrap | 
| colorAccording2 | Transform Numeric Values To Color-Gradient | 
| colSds | sd for each column | 
| combinatIntTable | Planing for making all multiplicative combinations | 
| combineAsN | Combine Vectors From List And Return Basic Count Statistics | 
| combineByEitherFactor | Create factor-like column regrouping data regrouping simultaneaously by two factors | 
| combineOverlapInfo | Find and combine points located very close in x/y space | 
| combineRedBasedOnCol | Combine/reduce redundant lines based on specified column | 
| combineRedundLinesInList | Combine Redundant Lines In List | 
| combineRedundLinesInListAcRef | Combine Redundant Lines In List, Deprecated | 
| combineReplFromListToMatr | Combine replicates from list to matrix | 
| combineSingleT | Get all combinations with TRUE from each column | 
| completeArrLst | Complete list of arrays for same dimensions | 
| concatMatch | Value Matching With Option For Concatenated Terms | 
| confInt | Confidence Interval To Given Alpha | 
| contribToContigPerFrag | Characterize individual contribution of single edges in tree-structures | 
| conv01toColNa | Convert matrix of integer to matrix of x-times repeated column-names | 
| convColorToTransp | Assign new transparency to given colors | 
| convMatr2df | Convert matrix (eg with redundant) row-names to data.frame | 
| convToNum | Convert Vector To Numeric | 
| coordOfFilt | get coordinates of values/points in matrix according to filtering condition | 
| correctToUnique | Correct vector to unique | 
| correctWinPath | Correct mixed slash and backslash in file path | 
| countCloseToLimits | Count from two vectors number of values close within given limits | 
| countSameStartEnd | Count same start- and end- sites of edges (or fragments) | 
| cutArrayInCluLike | Cut 3-dim array in list of matrixes (or arrays) similar to organizing into clusters | 
| cutAtMultSites | Cut character-vector at multiple sites | 
| cutToNgrp | Cut numeric vector to n groups (ie convert to factor) | 
| diffCombin | Compute matrix of differences for all pairwise combinations of numeric vector | 
| diffPPM | Difference in ppm between numeric values | 
| elimCloseCoord | Eliminate close (overlapping) points (in x & y space) | 
| equLenNumber | Equal character-length number | 
| exclExtrValues | Exclude extreme values (based on distance to mean) | 
| exponNormalize | Normalize by adjusting exponent | 
| extr1chan | Extract just one series, ie channel, of list of arrays | 
| extractLast2numericParts | Extract last two numeric parts from character vector | 
| extrColsDeX | Flexible extraction of columns | 
| extrNumericFromMatr | Extract numeric part of matrix or data.frame | 
| extrSpcText | Extract specific text | 
| filt3dimArr | Filter three-dimensional array of numeric data | 
| filterLiColDeList | Filter lines(rows) and/or columns from all suitable elements of list | 
| filterList | Filter for unique elements | 
| filterNetw | Filter nodes & edges for extracting networks This function allows extracting and filtering network-data based on fixed threshold ('limInt') and add sandwich-nodes (nodes inter-connecting initial nodes) out of node-based queries. | 
| filtSizeUniq | Filter for unique elements | 
| findCloseMatch | Find close numeric values between two vectors | 
| findRepeated | Find repeated elements | 
| findSimilFrom2sets | Find similar numeric values from two vectors/matrixes | 
| findUsableGroupRange | Select groups within given range | 
| firstLineOfDat | Filter matrix to keep only first of repeated lines | 
| firstOfRepeated | Find first of repeated elements | 
| firstOfRepLines | Reduce to first occurance of repeated lines | 
| fuseAnnotMatr | Fuse annotation matrix to initial matrix | 
| fuseCommonListElem | Fuse content of list-elements with redundant (duplicated) names | 
| fusePairs | Fuse pairs to generate cluster-names | 
| get1stOfRepeatedByCol | Get first of repeated by column | 
| getValuesByUnique | Print matrix-content as plot | 
| gitDataUrl | Convert ulr-name for reading in raw-mode | 
| htmlSpecCharConv | Html Special Character Conversion | 
| keepCommonText | Extract Longest Common Text Out Of Character Vector | 
| levIndex | Transform (factor) levels into index | 
| linModelSelect | Test multiple starting levels for linear regression model, select best and plot | 
| linRegrParamAndPVal | Fit linear regression, return parameters and p-values | 
| listBatchReplace | Replacements in list | 
| listGroupsByNames | Organize values into list and sort by names | 
| lmSelClu | Run lm on segmented data (from clustering) | 
| lrbind | rbind on lists | 
| makeMAList | Make MA-List Object | 
| makeNRedMatr | Make non-redundant matrix | 
| matchMatrixLinesToRef | Match All Lines of Matrix To Reference Note | 
| matchNamesWithReverseParts | Value Matching with optional reversing of sub-parts of non-matching elements | 
| matchSampToPairw | Match names to concatenated pairs of names | 
| matr2list | Transform columns of matrix to list of vectors | 
| mergeMatrices | Merge Multiple Matrices | 
| mergeMatrixList | Merge Multiple Matrices from List | 
| mergeSelCol | Merge selected columns out of 2 matrix or data.frames | 
| mergeSelCol3 | mergeSelCol3 | 
| mergeVectors | Merge Named Vectors | 
| mergeW2 | Extended version of merge for multiple objects (even without rownames) | 
| minDiff | Minimum distance/difference between values | 
| moderTest2grp | Moderated Pair-Wise t-test From Limma | 
| moderTestXgrp | Multiple moderated pair-wise t-tests from limma | 
| multiCharReplace | Multiple replacement of entire character elements in simple vector, matrix or data.frame | 
| multiMatch | Simple Multi-to-Multi Matching of (Concatenated) Terms | 
| naOmit | Fast na.omit | 
| nFragments | Number of fragments after cut at specific character(s) within size-range | 
| nFragments0 | Number of fragments after cut at specific character(s) | 
| nNonNumChar | Count number of non-numeric characters | 
| nonAmbiguousMat | Transform matrix to non-ambiguous matrix (in respect to given column) | 
| nonAmbiguousNum | Make numeric vector non-ambiguous (ie unique) | 
| nonredDataFrame | Filter for unique elements | 
| nonRedundLines | Non-redundant lines of matrix | 
| normalizeThis | Normalize Data In Various Modes | 
| numPairDeColNames | Extract pair of numeric values from vector or column-names | 
| orderMatrToRef | Order Lines of Matrix According to Reference (Character) Vector | 
| organizeAsListOfRepl | (re)organize data of (3-dim) array as list of replicates | 
| packageDownloadStat | Simple Package Download Statistics From CRAN | 
| pairsAsPropensMatr | Convert Pairs of Node-Names to Non-Oriented Propensity Matrix | 
| partialDist | Partial distance matrix (focus on closest) | 
| partUnlist | Partial unlist of lists of lists | 
| pasteC | Advanced paste-collapse | 
| presenceFilt | Filter lines of matrix for max number of NAs | 
| presenceGrpFilt | Filter for each group of columns for sufficient data as non-NA | 
| protectSpecChar | Protect Special Characters | 
| pVal2lfdr | Convert p-values to lfdr | 
| randIndFx | Distance of categorical data (Jaccard, Rand and adjusted Rand index) | 
| rankToContigTab | Contingenty tables for fit of ranking | 
| ratioAllComb | Calculate all ratios between x and y | 
| ratioToPpm | Convert ratio to ppm | 
| readCsvBatch | Read batch of csv-files | 
| readTabulatedBatch | Batch Reading Of Tabulated Text-Files | 
| readVarColumns | Read Tabular Content Of Files With Variable Number Of Columns | 
| readXlsxBatch | Read Batch of Excel xlsx-Files | 
| reduceTable | Reduce table by aggregating smaller groups | 
| regrBy1or2point | Rescaling according to reference data using linear regression. | 
| regrMultBy1or2point | Rescaling of multiple data-sets according to reference data using regression | 
| renameColumns | Rename columns | 
| reorgByCluNo | Reorganize matrix according to clustering-output | 
| replicateStructure | Search and Select Groups of Replicates | 
| replNAbyLow | Replace NAs by low values | 
| replPlateCV | CV of replicate plates (list of matrixes) | 
| rmDupl2colMatr | Remove lines of matrix redundant /duplicated for 1st and 2nd column | 
| rmEnumeratorName | Remove or rename enumerator tag/name (or remove entire enumerator) from tailing enumerators | 
| rmOrphans | Remove or Reassign Orphan Indexes | 
| rmSharedWords | Trim/Remove Redundant Words | 
| rnormW | Normal random number generation with close fit to expected mean and sd | 
| rowCVs | rowCVs | 
| rowGrpCV | Row group CV | 
| rowGrpMeans | rowMeans with destinction of groups (of columns, eg groups of replicates) | 
| rowGrpNA | Count number of NAs per row and group of columns | 
| rowGrpSds | Per line and per group sd-values | 
| rowGrpSums | rowSums with destinction of groups (of columns, eg groups of replicates) | 
| rowMedSds | Estimate sd Of Median For Each Row By Bootstrap | 
| rowNormalize | Row Normalize | 
| rowSds | sd for each row (fast execution) | 
| rowSEMs | SEM for each row | 
| sampNoDeMArrayLM | Locate Sample Index From Index Or Name Of Pair-Wise Comparisons In List Or MArrayLM-Object | 
| scaleXY | Scale data to given minimum and maxiumum | 
| searchDataPairs | Search duplicated data over multiple columns, ie pairs of data | 
| searchLinesAtGivenSlope | Search Points Forming Lines At Given Slope | 
| simpleFragFig | Simple figure showing line from start- to end-sites of edges (or fragments) defined by their start- and end-sites 'simpleFragFig' draws figure showing start- and end-sites of edges (or fragments) | 
| singleLineAnova | 2-factorial Anova on single line of data | 
| sortBy2CategorAnd1IntCol | Sort matrix by two categorical and one integer columns | 
| sortByNRepeated | Make a list of common occurances sorted by number of repeats | 
| stableMode | Estimate Mode (Most Frequent Value) | 
| standardW | Standardize (scale) data | 
| stdErrMedBoot | Standard Eror Of Median by Boot-Strap | 
| summarizeCols | Summarize columns (as median,mean,min,last or other methods) | 
| sumNAperGroup | Count number of NAs per sub-set of columns | 
| sysDate | System-date (compressed format) | 
| tableToPlot | Print matrix-content as plot | 
| test2factLimma | 2-Factorial Limma-Style t-Test | 
| top3mean | Mean Of 3 Highest Values | 
| transpGraySca | Make single vector gray-gradient | 
| treatTxtDuplicates | Locate duplicates in text and make non-redundant | 
| triCoord | Pairwise x,y combinations | 
| trimmedMean | Trimmed Mean | 
| trimRedundText | Trim redundant text | 
| tTestAllVal | t.test on all individual values against all other values | 
| unifyEnumerator | Unify Enumerators | 
| uniqCountReport | Report number of unique and redundant elements (optional figure) | 
| upperMaCoord | (upper) pairwise x,y combinations | 
| withinRefRange | Check for values within range of reference | 
| writeCsv | Write (and convert) csv files | 
| XYToDiffPpm | Express difference as ppm | 
| .addLetterWoLast | Add letter to all elements but not last | 
| .allRatioMatr1to2 | Calculate ratios for each column to each column of reference-matrix | 
| .allRatios | Search character-string and cut either before or after | 
| .arrLstMean | Summarize along columns of multiple arrays in list | 
| .arrLstSEM | Summarize along columns of mult arrays in list | 
| .asDF2 | Convert anything to data.frame | 
| .breakInSer | Get series of values after last discontinuity | 
| .bringToCtr | Bring most extreme to center | 
| .checkArgNa | Check argument names | 
| .checkConsistentArrList | Check list of arrays for consistent dimensions of all arrays | 
| .checkConvt2Vect | Convert to simple vector (similar to unlist) | 
| .checkFactor | Check Factor | 
| .checkFileNameExtensions | checkFileNameExtensions Function for checking file-names. | 
| .checkLegendLoc | Check argument for Location of legend | 
| .checkLmConfInt | Compare 'dat' to confindence interval of linare model 'lMod' (eg from lm()) | 
| .checkRegrArguments | Check regression arguments | 
| .chooseGrpCol | Automatic choice of colors | 
| .combineListAnnot | Combine annotation information from list of matrixes | 
| .compareByDiff | Compare by distance/difference | 
| .compareByLogRatio | Compare by log-ratio | 
| .compareByPPM | Compare by PPM | 
| .complCols | Search (complementing) columns for best coverage of non-NA data for rowNormalization (main) | 
| .composeCallName | Compose sequence of (function-)calls | 
| .convertMatrToNum | Convert numeric matrix to numeric | 
| .convertNa | Convert/standardize names of 'query' to standard names from 'ref' | 
| .corDuplItemsByIncrem | Avoid duplicating items between 'curNa' and 'newNa' by incrementing digits after 'extPref' (in newNa) | 
| .cutAtSearch | Search character-string and cut either before or after | 
| .cutStr | Cut string to get all variants from given start with min and max length | 
| .datSlope | Model linear regression and optional plot | 
| .doubleExt | Return File-name Extensions Including Double Extensions (eg txt.gz) | 
| .extrNAneighb | Extract NA-neighbour values | 
| .extrNumHeadingCap | Extract number(s) before capital character | 
| .extrNumHeadingSepChar | Extract numbers before separator followed by alphabetic character | 
| .filterNetw | Filter nodes & edges for extracting networks (main) This function allows extracting and filtering network-data based on fixed threshold ('limInt') and add sandwich-nodes (nodes inter-connecting initial nodes) out of node-based queries. | 
| .filterSw | Filter 3-dim array of numeric data (main) | 
| .filtSize | Filter for size | 
| .findBorderOverlaps | Find overlap instances among range of values in lines | 
| .firstMin | Get first minimum | 
| .fuse2ArrBy2ndDim | fuse 2 instances of 3dim arr as mult cols in 3dim array | 
| .getAmean | Get A value for each group of replicates | 
| .getAmean2 | Get A value for each group of replicates based on comp | 
| .getMvalue2 | Get M value for each group of replicates based on comp | 
| .growTree | Grow tree | 
| .insp1dimByClustering | Segment (1-dim vector) 'dat' into clusters | 
| .inspectHeader | Inspect 'matr' and check if 1st line can be used/converted as header | 
| .keepCenter1d | Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping center of data | 
| .keepFiniteCol | Remove all columns where all data are not finite | 
| .mayBeNum | Check if vector may be numeric content | 
| .medianSpecGrp | Rescale respective to specific group | 
| .mergeMatrices | Merge Multiple Matrices (main) | 
| .minDif | find closest neighbour to numeric vector | 
| .neigbDis | Distances beteenw sorted points of 2-columns | 
| .normalize | Main Normalization function | 
| .normConstSlope | Normalize columns of 2dim matrix to common linear regression fit | 
| .offCenter | Return position of 'di' (numeric vector) which is most excentric (distant to 0), starts with NAs as most excentric | 
| .pasteCols | Paste-concatenate all columns of matrix | 
| .plotCountPie | Pie plot for counting results | 
| .plusLowerCaps | Add lower caps to character vector | 
| .predRes | Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'dat' | 
| .raiseColLowest | Raise all values close to lowest value | 
| .removeCol | Remove columns indicated by col-number | 
| .removeEmptyCol | Search for (empty) columns conaining only entries defined in 'searchFields' and remove such columns | 
| .replSpecChar | Replace Special Characters | 
| .retain1stPart | Trim character string: keep only text before 'sep' | 
| .rowGrpCV | row group CV (main) | 
| .rowGrpMeans | row group mean (main) | 
| .rowGrpSds | row group sd (main) | 
| .rowGrpSums | row group rowSums per group (main) | 
| .rowNorm | Row-normalization procedure on matrix or data.frame 'dat' | 
| .rowNormFact | Obtain normalization factor (main) | 
| .scale01 | Scale between 0 and 1 (main) | 
| .scaleSpecGrp | Rescale respective to specific group | 
| .scaleXY | Scale between min and max value (main) | 
| .seqCutStr | Cut string to get all variants from given start with min length, depreciated | 
| .setLowestTo | Set lowest value to given value | 
| .sortMid | Choose most frequent or middle of sorted vector | 
| .stackArray | Reorganize array by reducing dimension 'byDim' (similar to stack() for data-frames) | 
| .summarizeCols | Summarize columns of matrix (or data.frame) 'x' using apply (main) | 
| .trimFromEnd | Trim from end (Deprecated) | 
| .trimFromStart | Trim from start (Deprecated) | 
| .trimLeft | Trim From Left Side | 
| .trimRight | Trim From Right Side | 
| .uniqueWName | Check regression arguments | 
| .vector2Matr | Convert numeric vector to matrix |