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