BioFSharp
BioFSharp Namespace
Type | Description |
IBioItem |
Marker interface for BioItem base. |
NcbiParsingType |
Lexer Tags for parsing BioItems |
Module | Description |
Alignment |
Basic structure and functionality for sequence alignments. Alignment functions can be found in the BioFSharp.Algorithm namespace. |
AminoAcidSymbols |
Contains the AminoAcidSymbol type and its according functions. The AminoAcidSymbol type is a lightweight, efficient presentation of amino acids |
AminoAcids |
Contains the AminoAcid type and its according functions. The AminoAcid type is a complex presentation of amino acids, allowing modifications |
AminoProperties |
Contains functionalities for obtaining included literary data on key amino acid properties |
BioArray |
This module contains the BioArray type and its according functions. The BioArray type is an array of objects using the IBioItem interface |
BioID |
Parsing Library for common biological ID formats like Cre(C.reinhardtii) or YeastId |
BioItem |
Basic functions on IBioItems interface |
BioItemsConverter |
Contains Functionalities for parsing Bioitems |
BioList |
This module contains the BioList type and its according functions. The BioList type is a List of objects using the IBioItem interface |
BioSeq |
This module contains the BioSeq type and its according functions. The BioSeq type is a sequence of objects using the IBioItem interface |
Digestion |
Contains types and functions needed to digest amino acid sequences with proteases |
Elements |
Contains chemical elements represented as a mixture of their stable isotopes and functionality for building them |
Formula |
Contains functionality for working with molecules as a formula of their elements and formulas of biologically relevant molecules |
GlobalModificationInfo | |
IsoelectricPoint |
Finding the isoelectric point of peptides |
Isotopes |
Contains functionality for working with and creating isotopes and list of biologically relevant isotopes |
IsotopicDistribution |
Contains functionality for working with isotopic abundancies of molecules |
Mass |
Molecular mass related functions |
ModificationInfo |
Functionality for creating formula modifications |
Nucleotides |
Contains the Nucleotide type and its according functions. |
PeptideClassification |
Contains functions to classify peptides based on their specificity when mapped to proteins |
PhylTree |
Phyologenetic Tree and functions |
PhysicalConstants |
Collection of physical constants |
Refactor | |
TaggedSequence | |
WorkflowLanguage |
BioFSharp.Algorithm Namespace
Module | Description |
PairwiseAlignment |
Contains functions for evaluating the best possible alignments for 2 Sequences |
ScoringMatrix |
Contains functions for using the included similarity matrices. These assign a score to every pair of aminoacids/nucleotides and therefore rate the probability of their substitution. The Scoring Matrices are generally used for alignments. |
StringMatching |
A collection of different string matching algorithms |
BioFSharp.BioContainers Namespace
Module | Description | ||
BioContainer |
BioContainer helper |
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BioContainerIO |
BioContainer helper |
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Blast |
DSLs for executing commands in the BLAST biocontainer Generated and tested for the tag blast:2.2.31--pl526h3066fca_3 |
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ClustalO | |||
Docker |
Docker helper |
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FastP | |||
HMMER |
HMMER - Biological sequence analysis using profile hidden Markov models (http://hmmer.org/) Functions providing an API for the HMMER 3 biocontainer |
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Hera | |||
IntaRNA | |||
LastAlign |
!! Currently many parameters are not implemented! From the Last docs at http://last.cbrc.jp: LAST finds similar regions between sequences. LAST can: Handle big sequence data, e.g:
Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA to proteins, with frameshifts. Compare PSSMs to sequences Calculate the likelihood of chance similarities between random sequences. Do split and spliced alignment. Train alignment parameters for unusual kinds of sequence (e.g. nanopore). |
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MoFF |
moFF is an OS independent tool designed to extract apex MS1 intensity using a set of identified MS2 peptides. It currently uses a Thermo library to directly extract data from Thermo Raw spectrum files,
eliminating the need for conversions from other formats. Moreover, moFF also allows to work directly with mzML files.
Input Data: moFF requires two types of input for the quantification procedure
Thermo RAW file or mzML file -and- MS2 identified peptide information.
The MS2 identified peptides can be presented as a tab-delimited file containing mimimal (mandatory) annotation for each peptide.
The tab-delimited file must contain the following information for all the peptides:
'peptide' : peptide-spectrum-match sequence
'prot' : protein ID
'mod_peptide' : peptide-spectrum-match sequence that contains also possible modification (i.e NH2-M |
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SRATools | |||
STAR | |||
TargetP | |||
Tmhmm |
TMHMM 2.0c predicts transmembrane helices in proteins |
BioFSharp.BioDB Namespace
Module | Description |
EbiAPI | |
Entrez | |
FaToolDb |
Tools for the odata service FaTools available at http://iomiqsweb1.bio.uni-kl.de/Services/FaToolDbDataService.svc |
GEO |
BioFSharp.IO Namespace
Module | Description |
AgilentRaw | |
BlastHits | |
BlastNCBI |
Blast Wrapper |
BlastQueries | |
Clustal |
Contains functions for reading clustal alignment files |
ClustalOWrapper |
Wrapper and its helpers for Clustal Omega multiple alignment tools |
FSIPrinters |
Pretty printers for various custom types in the library |
FastA | |
FastQ | |
GAF | |
GFF3 |
Contains functions for reading and writing GFF3 files |
GenBank |
functions for reading and writing GenBank files |
Mgf |
Mgf http://www.matrixscience.com/help/data_file_help.html`_ is a simple human-readable format for MS/MS data. It allows storing MS/MS peak lists and exprimental parameters. |
Newick |
Contains functions for parsing phylogenetic trees in the Newick format |
Obo |
Functions for par |
OrthoMCL | |
SOFT | |
WorkflowLanguage |
BioFSharp.ImgP Namespace
BioFSharp.ML Namespace
Module | Description |
DPPOP |
DPPOP - DeeP Peptide Observability Predictor. d::pPop uses a deep neural network to predict proteotypic peptides for proteins of interest. See the publication: https://www.frontiersin.org/articles/10.3389/fpls.2018.01559/full |
BioFSharp.Parallel Namespace
Module | Description |
PairwiseAlignment |
BioFSharp.Stats Namespace
Module | Description |
OntologyEnrichment | |
Sailent |
BioFSharp.Vis Namespace
Module | Description |
Chord | |
HtmlScaffold | |
Venn | |
ViewContainer |