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 |