miRBooking tagshttps://gitlab.iric.ca/major-lab/mirbooking/-/tagshttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.4.3v2.4.3Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.4.2v2.4.2v2.4.2
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.4.1v2.4.1v2.4.1
Fix API version
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.4.0v2.4.0v2.4.0
- assume LAPACK is always present and use it as a default solver
- add --sponged-fraction-cutoff and rename --relative-cutoff to --bound-fraction-cutoff
- use Yan et al. model by default and add a none option to --supplementary-model
- automatically locate score tables
- add explicit flags for FASTA flavours
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.3.0v2.3.0v2.3.0
This release brings a very nice set of features that makes miRBooking
more robust, efficient and convenient to use.
- add --version flag
- locate the default score tables automatically
- fold the seed with a mask and temperature
- add gene_accession and gene_name to the output format
- introduce a new tsv-detailed format
- add support for LAPACK and MKL LAPACK solvers
- reintroduce SuperLU MT solver
- select best available solver
- move I/O facilities in the broker
- add a blacklist filter system
- add a new mirbooking-iterative strategy to solve the system gradually
using the blacklist filter
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.2.3v2.2.3v2.2.3
Backport various improvements from the 2.3 series:
- install 1/2/3 mismatch score tables
- use installed 7mer-3mismatch table by default
- use installed 3mer (Yan et al.) or 4mer (Wee et al.) by default
- check for sparse solver availability at runtime
- fix parsing of gene names from NCBI FASTA
- remove SuperLU MT codepath that was not intended for 2.2 series
- add support for OpenBLAS and ATLAS flavours of CBLAS
- factor kother contribution into Km
- fix bug in target site vacancy formula
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.2.2v2.2.2v2.2.2
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.1.3v2.1.3v2.1.3
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.2.1v2.2.1v2.2.1
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v1.2.5v1.2.5v1.2.5
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.0.3v2.0.3v2.0.3
Fix CUDA root build issue.
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.2.0v2.2.0v2.2.0
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.1.2v2.1.2v2.1.2
- use 2.1 API version
- fix usage of 'cuda_root' option
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.1.1v2.1.1v2.1.1
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.1.0v2.1.0v2.1.0
- compute true vacancy using position factorization
- add API for retrieving various quantities and rates
- make the broker entirely reproducible from its publicly exposed state
- use standard masks for seed in generate-score-table
- rename 4-mer supplementary model to Wee et al. 2012
- use a struct for representing an interaction score
- use CBLAS (or MKL CBLAS) in odeint
- add support for PARDISO solver
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.0.2v2.0.2v2.0.2
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.0.1v2.0.1v2.0.1
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.0.0v2.0.0v2.0.0
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v2.0.0-alphav2.0.0-alphav2.0.0-alpha
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.comhttps://gitlab.iric.ca/major-lab/mirbooking/-/tags/v1.2.4v1.2.4v1.2.4
- speedup lookup in 5' direction when computing the vacancy
- fix missing nucleotide in 3'UTR footprint
- support GENCODE-style annotations
- generate a manpage with help2man
Guillaume Poirier-Morencyguillaumepoiriermorency@gmail.com