Add approaches based on pValue and qValue to generate present/absent calls
Default approach to generate calls is pValue
Add function “'merging_libraries“' allowing to merge calls per condition
Add function “'generate_slurm_indexes“' generating kallisto indexes on a cluster with slurm queing system
Add function “'generate_slurm_calls“' generating expression calls on a cluster with slurm queing system
Update documentation
Add ?BgeeCall documentation with link to main functions
Add verbose slot in UserMetadata
Add slots allowing not to rerun steps of the workflow. Do not rerun by default
Update documentation
New functionalties when running BgeeCall from list of libraries
Moved from workflow to software section
Better manage transcript version
Manage output directory when calls are generated for several libraries
Manage transcript version when calls are generated for several libraries
Change kmer size of kallisto index from 21 to 15 for libraries with readLength <= 50bp
Can choose the output directory
By default use a simpler arborescence for the output directory
Can use reference intergenic sequences generated by the community
Can use custom reference intergenic sequences from a local fastq file
Public release of BgeeCall package. Enjoy!!!