165 tool(s) found

Tool Description Topics Available version(s)
2DNMR_Annotation Annotation of complex mixture bidimensional NMR spectra 2
Add column to an existing dataset 3
Analytic correlation filtration : Detect analytic correlation among data and remove them. 1
Anova N-way anova. With ou Without interactions 3
ASCA Splitting of the total variance into independent blocks according to the experimental factors and multivariate analysis (SCA) of each block 1
bank_inhouse search by accurate mass (and by Retention time) on a local bank 2
Bar chart for multiple columns 1
Batch_correction Corrects intensities for signal drift and batch-effects 7
Between-table Correlation Correlation table between two tables and graphic representation 3
Bih4MaConDa : Utility to detect potential contaminants in your peak list based on MaConDa database 1
Biosigner Molecular signature discovery from omics data 2
Boxplot of quality statistics 2
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 11
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 12
Change Case of selected columns 1
Check Format Checking/formatting the sample and variable names of the dataMatrix, sampleMetadata, and variableMetadata files 4
Chemspider Search and share chemistry. 1
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Compare two Datasets to find common or distinct rows 1
Compute an expression on every row 4
Concatenate datasets tail-to-head 1
Convert delimiters to TAB 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 2
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to fai file 1
Convert FASTA to len file 2
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 2
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 2
Convert GFF to BED 2
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 2
Convert lped to fped 2
Convert lped to plink pbed 2
Convert MAF to Fasta 2
Convert MAF to Genomic Intervals 2
Convert Picard Interval List to BED6 converter 2
Convert plink pbed to ld reduced format 2
Convert plink pbed to linkage lped 2
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 2
Convert SAM to BAM 1
Convert tabular to dbnsfp 2
Convert uncompressed BCF to BCF 1
Count occurrences of each record 2
Create single interval as a new dataset 1
Cut columns from a table 2
Data Fetch 1
DEPRECATED ACP ellipsoid by factors 2
DEPRECATED CAMERA.annotate Wrapper function for the CAMERA annotate function (single class only). Returns annotation results (isotope peaks, adducts and fragments). 1
DEPRECATED metaMS.runGC GC-MS data preprocessing using metaMS package 1
DEPRECATED xcms.diffreport A report showing the most statistically significant differences in analyte intensities 1
Determine_batch_correction to choose between linear, lowess and loess methods 5
Filter data on any column using simple expressions Formatting 1
Find a mol file with a kegg id 1
Generic_Filter Removes elements according to numerical or qualitative values 4
Golm Metabolome Database search spectrum : GC-MS Mass Spectral Database. 2
Group data by a column and perform aggregate operation on other columns. 5
Heatmap Heatmap of the dataMatrix 3
Hierarchical Clustering using ctc R package for java-treeview 2
HMDB bank downloader : get a specific metabolite bank (as Urine...) from HMDB web portal. 1
HMDB MS search search by masses on HMDB online LCMS bank 3
HR2 formula find a chemical formula from a accurate mass 2
ID choice Choosing a particular column in your metadata to be considered as Identifiers 2
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Intensity Check Statistical measures, number of missing values and mean fold change 2
ISA to mzData Extract mzData files from an ISA dataset and output a collection of mzData dataset. 1
ISA to mzML Extract mzML files from an ISA dataset and output a collection of mzML dataset. 1
ISA to mzXML Extract mzXML files from an ISA dataset and output a collection of mzXML dataset. 1
ISA to netCDF Extract netCDF files from an ISA dataset and output a collection of netCDF dataset. 1
ISA to nmrML Extract nmrML files from an ISA dataset and output a collection of nmrML dataset. 1
ISA to W4M Convert ISA data type into W4M format 1
Isotope Correction for mass spectrometry labeling experiments 1
Join two Datasets side by side on a specified field 4
Kegg Compounds a Kyoto Encyclopedia of Genes and Genomes small molecules database. 1
LCMS matching Annotation of LCMS peaks using matching on a in-house spectra database or on PeakForest spectra database. 5
Line/Word/Character count of a dataset 1
Lipidmaps : search on LIPID MAPS Structure Database (LMSD) online with masses and its Text/Ontology-based search engine. 1
Merge Columns together 2
Metabolights downloader Import public and private MetaboLights studies 1
Metabolites Correlation Analysis 1
metaMS.plot GC-MS data preprocessing using metaMS package 1
metaMS.runGC GC-MS data preprocessing using metaMS package 5
mixmodel ANOVA for repeated measures statistics 1
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MSnbase readMSData Imports mass-spectrometry data files 4
msPurity.averageFragSpectra Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All) 1
msPurity.combineAnnotations Combine, score and rank metabolite annotation results 1
msPurity.createDatabase Create and SQLite database of an LC-MS(/MS) experiment 1
msPurity.createMSP Create MSP files from msPurity processed data 1
msPurity.dimsPredictPuritySingle Calculate the anticipated precursor ion purity from a DIMS dataset. 1
msPurity.filterFragSpectra Filter fragmentations spectra associated with an XCMS feature 1
msPurity.flagRemove Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds (e.g. RSD of intensity and retention time). 1
msPurity.frag4feature Assign fragmentation spectra to XCMS features using msPurity 1
msPurity.purityA Assess acquired precursor ion purity of MS/MS spectra 1
msPurity.purityX Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset. 1
msPurity.spectralMatching Perform spectral matching to MS/MS spectral libraries 1
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
Multivariate PCA, PLS and OPLS 6
NMR spectra alignment based on the Cluster-based Peak Alignment (CluPA) algorithm 3
NMR_Annotation Annotation of complex mixture NMR spectra and metabolite proportion estimation 1
NMR_Bucketing Bucketing and integration of NMR Bruker raw data 5
NMR_Normalization Normalization of NMR bucketed and integrated spectra 1
NMR_Preprocessing Preprocessing of 1D NMR spectra 3
NMR_Read Read Bruker NMR raw files 2
Normalization Normalization of (preprocessed) spectra 4
Paste two files side by side 1
ProbMetab Tool Wrapper function for ProbMetab R package. 3
proFIA Preprocessing of FIA-HRMS data 4
Quality Metrics Metrics and graphics to check the quality of the data 4
Remove beginning of a file 1
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 2
Select lines that match an expression 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Sort data in ascending or descending order 2
Summary Statistics for any numerical column 3
Table Merge Merging dataMatrix with a metadata table 3
Transformation Transforms the dataMatrix intensity values 3
Transpose data from a file 1
Trim leading or trailing characters 1
Univariate Univariate statistics 4
Upload File from your computer 2
Wiggle to Interval 2
xcms adjustRtime (retcor) Retention Time Correction 11
xcms fillChromPeaks (fillPeaks) Integrate areas of missing peaks 14
xcms findChromPeaks (xcmsSet) Chromatographic peak detection 14
xcms findChromPeaks Merger Merge xcms findChromPeaks RData into a unique file to be used by group 6
xcms get a sampleMetadata file which need to be filled with extra information 3
xcms groupChromPeaks (group) Perform the correspondence, the grouping of chromatographic peaks within and between samples. 13
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 4
xcms process history Create a summary of XCMS analysis 8