v1.15.12 minor modification in examples defining ExpressionSet instances
 

 bug fix in getCurves: the extend = 'pc1' option was broken in a non-obvious way (if endpoints of lineages are near 0 in dimensions 2+)
 

 remove suggested package from install 

 attempt to get biocstyle installed
 

 also warm up bioc devel cache?
 

 probably don't need these args if script is being overwritten
 

 third try
 

 try building without init
 

 remove html
 

 modified header of slingshot.Rmd (per suggestion on SO), rebuild vignette
 

 update migration_notes.md
 

 Fixed an error with non-matching seqlevels

 

 resync with Rsmatools 1.99.1 and Rhtslib 1.15.3
 

 Compile and link C code against Rhtslib instead of Rsamtools
 

 Fix for Solaris

Do not build standalone executables (e.g. bgzip, tabix, etc...). They're
not needed and seem to cause problems on Solaris.
 

 added sym2CellOnto function
 

 Fix ensemble import. Add IDR. See NEWs
 

 Added package logos to vignette
 

 bug fix: fixed bug introduced in previous patches when running create_sequences('RNA')
 

 bug fix: create_sequences(alphabet=RNA) now works with difreq/trifreq
 

 bug fix: create_sequences() not working properly with difreq or trifreq provided
 

 expanded add_multifreq() and compare_motifs() tests
 

 ctmarks app seems stable now
 

 Fix fetchExtendedChromInfoFromUCSC("hg38")

A recent change on the UCSC side broke
fetchExtendedChromInfoFromUCSC("hg38"), the workhorse behind
Seqinfo("hg38"). See https://support.bioconductor.org/p/117808/#117831
for the details. With this fix, hg38 is still strictly mapped to
GRCh38 and not to a patched version of it (what assembly hg38 is
based on exactly has become somewhat unclear on the UCSC side).
 

 revised ctmarks app with helpText
 

 (port) clean up Makevars
 

 better random number management on load

- don't create .Random.seed if not already present
 

 version
 

 fix the problem of compound/unannotated nodes causing graph merge fail
 

 version
 

 prototype definition and slots are consistent now, thanks to the reminder sent by Lori Shepherd
 

 Fixed bugs
 

 headTabix: use fread.gzipped only when user wants to get more than 1e6 rows
 

 methylRaw: check for content in tabix file, break if not
 

 calculateDiffMeth: dealing with case of full model not being different from reduced model; print warning and set NaN to 1
 

 improve validity checks for methylDB objects
 

 add test for methylRawList Constructor
 

 getCorrelation: reduce code duplication and overhead by introducing S3 functions to be called by S4 methods
 

 fread.gzipped: return df
 

 fread.gzipped: update function to check compression based on file content and allow to decompress .bgz files
 

 Update README.md

add codecov support 

 Update README.md 

 Bug in preproccessInputData solved (DESeqResults to data.frame)
 

 use UTF8
 

 parseKGML2DataFrame: edgeData and KEGGedgeData can be of different length. Now the solution is to expand the shorter one. users are encouraged to report any bug
 

 version bump
 

 renaming
 

 replace RUnit with testthat, add RCurl
 

 use testthat instead of RUnit as the test engine
 

 too long a line was truncated into shorter lines
 

 reduced size of PROonto.rda
 

 downsized TwoSzabo data set
 

 also give the validity score during custom gene set extractprojection()
 

 v1.1.22
 

 bug fix: scan_sequences() now works for motifs with pseudocount of 0
 

 updated news
 

 document() changed some documentation
 

 v1.11.8 minor vignette update
 

 testthat directory and eset slot in opls class
 

 1.15.11 : add sum as aggregation function
 

 v1.15.8; opls-eset: scores, loadings, VIP, etc. in pData and fData from getEset; parPaletteVc argument in plot-opls
 

 Remove knet_win32_init()/knet_win32_destroy() calls on Windows
 

 new version 1.15.10 to fix a bug in agregation stats
 

 minor change: fixed spelling mistakes + added lang field to desc
 

 changed the function of filterLowCountGenes.
 

 fixed windows build issues
 

 missing documentation
 

 add link to travis in status button 

 embed travis status in readme 

 fix comment
 

 merge
 

 add test to check that 'none' gets converted to NULL when passed for distributed
 

 extra paranthesis
 

 allow 'none' for distributed method
 

 ignore build files
 

 added check for params@distributed
 

 implemented policy based design for sparse/dense storage in the GibbsSampler
 

 replace names with patientID
 

 Merge remote-tracking branch 'origin/dev'
 

 version bump
 

 Update README.md 

 minor change: increased character param security + bug fix: method documentation for motif_tree()
 

 Consistent naming of RDS output files.
 

 Response to Issue #3: Prioritze rowData over empty Granges objects
 

 Added cbind to LoomGraphs documentation
 

 Bumped version number, date.
 

 Forgot to add references.
 

 Reorganized text, elaborated on the doublet score interpretation.
 

 new feature: motif_peaks()
 

 cleaned up code
 

 Merge branch 'master' into experimental
 

 documentation first draft
 

 Merge branch 'master' into experimental
 

 initial motif_peaks() function created
 

 basic implementation for finding significant motif peaks in sequence data
 

 basic cluster framework set up
 

 update .Rbuildignore
 

 More ENUM fixes
 

 Fix bug introduced in read ENUM/factor
 

 (port) configure file to add -lrt linking
 

 add configure.ac, src/Makevars.in to check librt for shm_open and link to it if needed
 

 docfixes and fix to kozaksequenceScore (#69)

 

 remove one migration leftover
 

 Migrate to Rhtslib (htslib 1.7) and to Rsamtools 1.99.0