Transformations


Name Short Description Language
AddStrain Add new strain Python
AminoAcidComposition Amino acid composition of a protein sequence (Generated by PluGen) C++
BAMContig Split BAM file into contigs C++
BAMSort Sort a BAM file C++
BEDContig Split BED file into contigs C++
BedWindow Sliding window for BED file C++
BigWigAverageOverBed Average of Bigwig over BED file C++
BigCat Multi-concatenator C++
BIOM2CSV Convert BIOM file to CSVA Python
BLASTJoin Join outputs from BLAST C++
ClosestBED Search for overlapping features between two BED files C++
ComplementBED Complement BED file C++
CoverageBED Coverage in second BED from first C++
CSVCat Concatenate two CSVs Python
CSVCoarseFine Coarse and fine level CSV summations Python
CSVCol Extract columns from CSV Python
CSVColumnQuote Quote columns of CSV Python
CSVCrack Crack open a CSV (remove borders) Python
CSVHead Head of every CSV row Python
CSVMap Map bacterial names in CSV file Python
CSVReplace Take a CSV file, and replace one value by another Python
CSVSmooth Smooth filtered CSVs Python
CSVSubtract Subtract the contents of two CSV files Python
ChangeLevel Change phylogenetic analysis level R
CLR Center Log Ratio (CLR) transformation R
CombineAbundance Combine abundances from multiple samples Python
Copy Make a copy of a file Python
CSVAppend Append a new row or column to a CSV file Python
CSVCollate Collate a set of CSV files into one Python
CSVComma Pad CSV with comma Python
CSVJoin Database join Python
CSVJoinSplit Generate taxonomically classified taxa counts from original counts, metadata and taxonomic tree R
CSVLabel Label rows of a CSV file Python
CSVLast2First Move the last column of a CSV file to the first Python
CSVMapRange Map Range of One CSV File To Another (Useful in Multi-Omics) Python
CSVMerge Merge Multiple CSV Files Python
CSVMult Multiply a CSV file by a constant Python
CSVNormalize CSV Normalization Python
CSVPad CSV Padding Python
CSVPool Take a CSV and pool together duplicate rows/columns Python
CSVQuote Add quotes to row and column headers Python
CSVRemoveQuotedCommas Remove commas from inside quoted strings in CSV file Python
CSVRename Rename rows and/or columns of a CSV Python
CSVScale Scale CSV Values to Have a Median of One Python
CSVSort Sort a CSV file by row Python
CSVTranspose Transpose a Matrix in a CSV File Python
CSVUnNormalize CSV Reverse Normalization Python
CSVUnPad Remove CSV padding Python
CSVUnQuote Remove quotes from CSV file Python
CSVZero2Min Change All Zeroes in a CSV to the Minimum Value Python
CreateGroupings Create groupings for a dataset Python
DBUnroll Unroll a database Python
Dereplication Convert redundant reads into sequences and counts R
DGEList Convert input to DGEList format R
DNA2Protein Corresponding protein for DNA sequence Python
DNAComplement Complement a DNA sequence Python
DNAReverseComplement Reverse complement a DNA sequence Python
FASTACat Concatenate FASTA files Python
FASTAClean Remove metacharacters from FASTA headers Python
FASTAEven Even lines of FASTA file C++
FASTAREGEX Search FASTA for regular expression Perl
FASTAReplace Replace sequence names with OTU Python
FASTAShard Split a FASTA file into shards Python
FASTQContig Split FASTQ file into contigs C++
GMLMap Map bacterial names in GML file Python
GeneUnify Unify gene expression values across multiple files R
Head Top n entries (typically of a feature list) R
Hellinger Hellinger transform (Hellinger et al, 1914) R
IDXShard Split an index into shards C++
IntersectBED Intersect two BED files C++
IRLBA Fast truncated SVD R
KronaReplace Replace a string in a Krona file by another string Python
LEfSeKeepUnique Keep only unique taxa in LEfSe input Python
LEfSeUnClassified Rename unclassified taxonomies Python
LabelDups Take a CSV file and label duplicate entries Python
Linear Linear model fit R
LinksBED Lookup known gene in UCSC browser C++
Log1P Transform data by log(1) R
Log10 Transform data by log base 10 R
Log10P Transform data by log(1+x) R
LogTransform Log-transform data Python
Map2Positive Map All Edges To Positive Range Python
MaskFASTAFromBED Mask FASTA based on BED intervals C++
MergeBED Merge BED files C++
MergeFiles Merge the content of all files that match a pattern Python
MergePairedEnd Merge paired-end reads R
MergeSRA Merge FASTQ files listed in an SRA input Python
MetaPrefix Metadata based on prefix Python
MetabNorm Mixed-Mode (Cohort and Batch) Metabolite Normalization (Jauhiainen et al, 2014) R
MetaPhlAnSplit Split MetaPhlAn (Beghini et al, 2021) taxonomy into phylogenetic classifications Python
NewickFixAdjacent Fix adjacent nodes of Newick tree Python
NOAMap Map bacterial names in NOA file Python
NormScoreTransform Normal Probability Values R
Oksanen Oksanen transformation (Oksanen, 1983) R
Overlap Amount of overlap between BED and genome C++
ParseUnique Output unique bacteria Perl
Permute Permute taxa abundances Python
PhyloSeqMark Take PhyloSeq (McMurdie and Holmes, 2013) and mark elements Python
PhyloSeqMerge Merge PhyloSeq (McMurdie and Holmes, 2013) data Python
PhyloSeqNAResolve Take PhyloSeq (McMurdie and Holmes, 2013) taxonomy table and resolve all unclassifiable levels Python
PhyloSeqNormalize Normalize PhyloSeq (McMurdie and Holmes, 2013) taxa Python
PhyloSeqRemoveNull Remove null character from PhyloSeq (McMurdie et al, 2013) data C++
PhyloSeqReorder Reorder PhyloSeq (McMurdie and Holmes, 2013) taxa to correspond to metadata Python
PreprocessClinical Clinical data preprocessor Python
Rank Converts a set of counts to ranks in a sample Python
Rank2Tax Convert header of PhyloSeq (McMurdie et al, 2013) taxonomy table to use phylogeny Python
RDPChop Split an RDP (Cole et al, 2014) database Perl
RemoveBothTails Remove tails of FASTA sequences Python
RemoveHeader Remove header from CSV Python
RemovePrimer Remove primers (Quince et al, 2011) C++
SAMMerge Merge SAM paired-end reads Perl
SampleExtract Extract sample names from FASTQ files Python
ScaleCenter Scale and center the data R
SeparateGroups Separate samples into groups Python
ShortenNames Shorten bacterial names Python
SlopBED Slop a fixed number of bases C++
SortBED Sort a BED file C++
SortForwardReverse Sort forward and reverse reads to be in the same order Python
SortSamples Sort a set of samples by a property Python
SortWithTemp Sort FASTA with intermediate temporary C++
SplitBIOM Take a BIOM File and split it into each taxonomic tree level Python
SplitByLineCount Split FASTA by line count Python
SplitTableProcessing Take a table of counts from Mothur and split into multiple counts classified by taxonomy Python
StandardScaler StandardScaler (Raju et al, 2020) normalization Python
SubtractBED Subtract a second BED from the first C++
Standardize Transform to standard distribution R
TAB5Shard Split a TAB5 file into shards Python
TSV2KEGG Convert KEGG identifiers to pathway names Python
TSVRemove Remove rows and columns from TSV file Python
TaxonomySplit Take a table of abundances and make multiple, one for each level of the taxonomic tree Python
Transform Shift composition (Egozcue and Pawlowski-Glahn, 2016) Python
TSVPerturb Perturb values in TSV file Python
VST Standardized values R
WindowBED Find features in BED within a window C++
Z Z-transformation R
Zero2One Perturb zeroes to ones Python

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