| 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 |
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|
2 |
| CML to mol2 |
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|
2 |
| CML to SDF |
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|
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 |
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|
1 |
| Convert BED to Feature Location Index |
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|
1 |
| Convert BED to GFF |
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|
2 |
| Convert Biom1 to Biom2 |
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|
1 |
| Convert Biom2 to Biom1 |
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|
1 |
| Convert FASTA to 2bit |
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|
2 |
| Convert FASTA to Bowtie base space Index |
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|
1 |
| Convert FASTA to Bowtie color space Index |
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|
1 |
| Convert FASTA to fai file |
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|
1 |
| Convert FASTA to len file |
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|
2 |
| Convert FASTA to Tabular |
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|
1 |
| Convert Genomic Intervals To BED |
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|
1 |
| Convert Genomic Intervals To Coverage |
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|
2 |
| Convert Genomic Intervals To Strict BED |
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|
2 |
| Convert Genomic Intervals To Strict BED12 |
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|
1 |
| Convert Genomic Intervals To Strict BED6 |
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|
2 |
| Convert GFF to BED |
|
|
2 |
| Convert GFF to Feature Location Index |
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|
1 |
| Convert Len file to Linecount |
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|
2 |
| Convert lped to fped |
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|
2 |
| Convert lped to plink pbed |
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|
2 |
| Convert MAF to Fasta |
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|
2 |
| Convert MAF to Genomic Intervals |
|
|
2 |
| Convert Picard Interval List to BED6 |
converter |
|
2 |
| Convert plink pbed to ld reduced format |
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|
2 |
| Convert plink pbed to linkage lped |
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|
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 |
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|
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 |
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|
2 |
| InChI to MOL |
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|
2 |
| InChI to MOL2 |
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|
2 |
| InChI to SDF |
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|
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 |
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|
2 |
| MOL to SMILES |
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|
2 |
| MOL2 to CML |
|
|
2 |
| MOL2 to InChI |
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|
2 |
| MOL2 to MOL |
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|
2 |
| MOL2 to SDF |
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|
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 |