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NEWS
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NEWS
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0.1.0 (01-09-2017)
+ Code has been tested and is stable. Preparing for submission to Bioconductor once vignette (and various other requirements) is complete.
0.2.0 (01-18-2017)
+ Vignette completed testing
0.99.0 (01-20-2017)
+ Package (version 0.99.0) submitted to Bioconductor for review
0.99.2 (02-24-2017)
+ Revised package (version 0.99.2) submitted to Bioconductor for further review
0.99.2 (04-18-2017)
+ Revised package (version 0.99.2) submitted to Bioconductor for review
1.0.0 (04-19-2017)
+ Package accepted (version 1.0.0) at Bioconductor, included in version 3.5.
1.2.0 (09-26-2017)
+ Support added for the analysis of ESTs/cDNAs; BED files can now be provided as input (version 1.2.0)
1.2.1 (10-17-2017)
+ Minor changes in documentation to better reflect updates in v. 1.2 (version 1.2.1).
1.8.0 (07-10-2018)
+ Additional promoter (TSR) metrics added to output, including the modified shape index (mSI) and torque.
+ Modifications to column IDs to reflect updated nomenclature.
+ Updates to User's Guide in addition to creation of Singularity recipe for reproucible analysis across platforms.
1.8.9 (10-08-2018)
+ Updates that correct a speed issue encountered when analyzing data aligned to assemblies with many scaffolds.
+ Simplified part of one vignette.
1.10.12 (09-17-2019)
+ Updates to include 3'-read capturing from bam input files and data structures to allow ignoring spurious TSSs.
+ Added capabilities for sorting by strand (and seq/TSS) for TSS merging.
+ Made a change leading to a substantial speed-up of mergeSampleData().
+ Added qname to saved columns from .bam input.
+ Minor changes to writeTSR() and writeTSS().
+ Rewrite to mergeSampleData).
+ Improvements to loadTSSobj().
+ Necessary updates to the Singularity recipe to reflect the above changes.
1.13.1 (10-31-2019)
+ Version bump due to release of Bioconductor v. 3.10.
1.13.2 (11-01-2019)
+ Corrected minor bugs in non-user-level functions detTSR() and detTSS()
+ Various updates to Show-methods.R
1.13.3 (11-21-2019)
+ Updated documentation for loadTSSobj() for the sake of clarity.
1.13.4 (12-16-2019)
+ Added feature to writeTSS() that generates two separate bedgraph files (plus and minus) instead of one.
1.13.5 (3-30-2020)
+ Corrected line in loadTSSobj() that caused a build error in the Bioc devel branch (3.11).
1.15.1 (3-27-2020)
+ Version bump due to release of Bioconductor v. 3.11.
1.17.0 (10-27-2020)
+ Version bump due to release of Bioconductor v. 3.12.
1.17.2 (12-21-2020)
+ Updates to Singularity build and software
1.17.3 (2-12-2020)
+ Updates to DESCRIPTION, NEWS and README