141 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Anova N-way anova. With ou Without interactions 5
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 masses on local bank 1
Bar chart for multiple columns 1
Batch_correction Corrects intensities for signal drift and batch-effects 8
Biosigner Molecular signature discovery from omics data 3
Boxplot of quality statistics 1
CAMERA.annotate CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition. 7
CAMERA.combinexsAnnos Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations. 7
Change Case of selected columns 1
Check Format Checks the formats 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 3
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 1
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 1
Convert FASTA to Tabular 1
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
Count occurrences of each record 1
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 Pool Control Analyses data to check its quality according to: CV 1
DEPRECATED Quality Control Analyses data to check its quality according to: CV 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. 1
Group data by a column and perform aggregate operation on other columns. 2
Heatmap Heatmap of the dataMatrix 3
Hierarchical Clustering using ctc R package for java-treeview 2
HMDB MS search search by masses on HMDB online bank 2
HR2 formula find a formula for the masses 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Join two Datasets side by side on a specified field 2
Kegg Compounds a Kyoto Encyclopedia of Genes and Genomes small molecules database. 1
LC/MS matching Annotation of MS peaks using matching on a spectra database. 7
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
MassBank : High Quality Mass Spectral Database. 1
MassBank spectrum searches : Search by pseudo-spectra on a High Quality Mass Spectral Database. 1
match_mass search by masses on local bank 1
Merge Columns together 2
Metabolites Correlation Analysis 1
metaMS.runGC GC-MS data preprocessing using metaMS package 3
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 1
Multilevel Data transformation: Within matrix decomposition for repeated measurements (cross-over design) with mixOmics package 1
Multivariate PCA, PLS and OPLS 7
NMR_Alignment Alignment of NMR spectra 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 NMR raw files 2
Normalization Normalization of (preprocessed) spectra 3
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 1
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 2
Transformation Transforms the dataMatrix intensity values 4
Transpose data from a file 1
Trim leading or trailing characters 1
Univariate Univariate statistics 6
Upload File from your computer 2
Wiggle to Interval 1
xcms plot chromatogram Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s) 1
xcms.fillPeaks Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas 9
xcms.group Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. 9
xcms.retcor Retention Time Correction using retcor function from xcms R package 8
xcms.summary Create a summary of XCMS analysis 6
xcms.xcmsSet Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis 11
xcms.xcmsSet Merger Merge xcms.xcmsSet xset in one to be used by group 3