BioFSharp


BioFSharp

BioFSharp Namespace

TypeDescription
IBioItem

Marker interface for BioItem base.

NcbiParsingType

Lexer Tags for parsing BioItems

ModuleDescription
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

ModuleDescription
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

ModuleDescription
BioContainer

BioContainer helper

BioContainerIO

BioContainer helper

Blast

DSLs for executing commands in the BLAST biocontainer

Generated and tested for the tag blast:2.2.31--pl526h3066fca_3

ClustalO
Docker

Docker helper

FastP
HMMER

HMMER - Biological sequence analysis using profile hidden Markov models (http://hmmer.org/) Functions providing an API for the HMMER 3 biocontainer

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:

1: 
2: 
3: 
 - Compare two vertebrate genomes

 - Align billions of DNA reads to a genome

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).

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-MLTKFESK-COOH ) 'rt': peptide-spectrum-match retention time (i.e the retention time contained in the mgf file; The retention time must be specified in second) 'mz' : mass over charge 'mass' : mass of the peptide 'charge' : charge of the ionized peptide. ------ Argentini et al. Nature Methods. 2016 12(13):964–966.

SRATools
STAR
TargetP
Tmhmm

TMHMM 2.0c predicts transmembrane helices in proteins

BioFSharp.BioDB Namespace

ModuleDescription
EbiAPI
Entrez
FaToolDb

Tools for the odata service FaTools available at http://iomiqsweb1.bio.uni-kl.de/Services/FaToolDbDataService.svc

GEO

BioFSharp.IO Namespace

ModuleDescription
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

ModuleDescription
Centroid
Marr
Ricker
Trace

BioFSharp.ML Namespace

ModuleDescription
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

ModuleDescription
PairwiseAlignment

BioFSharp.Stats Namespace

ModuleDescription
OntologyEnrichment
Sailent

BioFSharp.Vis Namespace

ModuleDescription
Chord
HtmlScaffold
Venn
ViewContainer
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