Additions:
- BioFSharp.BioDD:
- Bugfixes:
- BioFSharp.BioContainers:
- fix fastP DSL command line generation (missing
=signs)
- fix fastP DSL command line generation (missing
- BioFSharp.BioContainers:
Additions:
- BioFSharp.BioContainers:
- Add fasterq-dump and prefetch DSL for the SRATools biocontainer
- Add full STAR RNASeq aligner DSL for the respective BioContainer. Commit details
- BioFSharp.IO:
- Add load script for referencing pretty printers, included in the nuget package
- Add multiple new pretty printers for SOFT
Bugfixes:
- BioFSharp.IO:
- BioFSharp.Stats:
- Massively improved SAILENT characterization speed for preprocessing of large datasets
- BioFSharp.BioContainers:
- BioFSharp.IO:
- Refactored SOFT Parser and improved its namespace encapsulation.
- add prettyPrinters for the SOFT GSE/GPL type](https://github.com/CSBiology/BioFSharp/pull/83/commits/615dcbfd30632d6fdf7a70edae9f5227ce250937)
- BioFSharp.BioDB:
- Fix FaTool OData model URL
- BioFSharp.Vis
- Add Function to save chord plots as html files
- BioFSharp.Stats:
- Major speed improvements for Sailent
Renaming of BioFSharp.Biotools makes this a major version increase, as it is not backwards compatible. Several bugfixes and additions to multiple sub projects:
-
We now have a cool new logo! (See readme)
-
BioFSharp.BioTools has been renamed to BioFSharp.BioContainers. This reflects the purpose of the library better than the previous name.
-
BioFSharp.BioContainers
- Add thin LastAlign biocontainer API wrapper
-
BioFSharp.IO
- Bugfixes:
- Fix SOFT parser skipping entities (fixes #72)
- Bugfixes:
-
BioFSharp.Stats
- Sailent is now faster and has a verbose option (fixes #74,#75)
-
BioFSharp.ImgP
- Add functionality to isolate local maxima from frames
- Add functionality to get correlation at specified coordinates
Several bugfixes and additions to multiple sub projects:
-
BioFSharp (core):
- Addition of various Unit tests (see the issue to track what has been added since the last version)
- Bugfixes:
-
BioFSharp.Stats
Several bugfixes and additions to multiple sub projects:
-
BioFSharp (core):
- Add Unit testing for modules: Formula Mass BioArray
- Changed functionality:
- Formula.substract now also returns negative atom counts
-
BioFSharp.ML:
- Additional functionality:
- add thin CNTK API
- Additional functionality:
Several bugfixes and additions to multiple sub projects:
-
BioFSharp (core):
- Additional functionality:
- GravyScore (Grand Average of Hydropathy) as additional amino acid property
- Additional functionality:
-
BioFSharp.IO:
-
Additional functionality:
- GAF Parser for GO Annotation file format: Gene Association File
- Uniprot style Fasta header parser
- FastA to GFF3 converter functions
- GFF3 Pretty Printer
-
BugFixes:
- Fix OboParser just taking the last occurence of the alt_id keyword and discards previous ones.
- Fix Fasta and GFF3 writers appending to files instead of recreating
-
-
BioFSharp.BioTools:
-
Additional functionality:
- TMHMM biocontainer API wrapper (TMHMM 2.0c predicts transmembrane helices in proteins)
- FastP and Hera biocontainer API wrapper
- IntaRNA biocontainer API wrapper (IntaRNA is a tool for prediction of various nucleotide interactions)
-
BugFixes:
- Fix Stream entry closed error in BioContainer.tarOfStream()
-
-
BioFSharp.ImgP:
-
Additional functionality:
-
Bugfixes:
-
- Fix template files for all nuget packages:
- use correct paths for binaries
- update project descriptions
- use type project to infer dependencies
- BioFSharp.ML - project introduction:
- Usage of Microsoft's CNTK library with a biological focus:
- This project comes with working CNTK integration:
- necessary dependencies to use CNTK and its unmanaged libraries
- CNTK loadscript: an easy way to load all dependencies of CNTK. load the script and use the resolveCNTKDependencies() function.
- Built-in deep neural network 'd::ppop' (publication)
- predict peptide observability in mass spectrometry
- Classification: functions to determine peptide feature vectors as input for dppop
- Prediction: functions to predict peptide observability using the feature vectors prepared in Classification.
- NonPlant and Plant models as embedded resources: the two models used in the original Web API. Additionally load custom models.
- Othert additions:
- BioFSharp.BioTools:
- Integration of new tools as biocontainer APIs:
- Hera
- FastP
- ClustalO
- HMMER (experimental):
- hmmbuild
- hmmalign
- hmmsearch
- hmmscan
- hmmemit
- hmmpress
- hmmconvert
- Integration of new tools as biocontainer APIs:
- BioFSharp.BioTools:
- Addition of blast biocontainer support for makeblastdb, blastp, blastn with full parameter wrapping
- Extension of BioContainer functionality:
- Add windows/unix path conversions and subpath matching to MounInfo
- Add execReturnAsync (returns stdout of docker container) and execAsync (redirects stdout/stderr of container)
- Addition of the BioTools project, which uses docker.dotnet to use docker images and stream their output to fsi
- Low level wrapping of multiple docker.dotnet functions for F#
- Basic functionality for using docker images from fsi
- Addition of Pretty Printers, SOFT Parser, GEOFTP functions
- Improvement and refactoring of Modification functionality
- ImgP - project introduction
- Initial release