Merge remote-tracking branch 'upstream/master'
 

 increase version number - correct
 

 Update full-power.Rmd
 

 Update NEWS
 

 Merge pull request #183 from databio/dev

Version 1.3.1 

 biocheck notes fix
 

 Updated example datasets for building gene models from custom genomes
 

 updated NEWS
 

 Merge pull request #181 from databio/dev_jose

Dev jose 

 paramater description update
 

 #176 fixed guides(fill = "none")
 

 Merge branch 'dev' of github.com:databio/GenomicDistributions into dev
 

 Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #176
 

 Update chrom bins plots
 

 Add new, faster implementation of calcCChromBinsRef
 

 fix partition overlap frequency count - multi input
 

 change size/position of pval labels
 

 use tidy directly from broom
 

 today date
 

 update version for next release
 

 Added option to set ylim in plotChromBins

- even one extreme bin size makes the plotChromBins output less usable
  - e.g. if most bins N ~10-100 and one is 8000 everything is scaled for this one bar (ran into this twice now in my work)
- instead of having to manually remove data one can simply set the ylim manually using the new ylim option 

 Add corrected neighbor dist, nearestNeighbors, doc changes
 

 0.20 partial responce to review
 

 0.19 partial responce to review
 

 0.19 partial responce to review
 

 0.18 partial responce to review
 

 0.40 partial responce to review
 

 0.38 tidy up
 

 0.36 tidy up
 

 looking for the bottleneck 0.34
 

 v0.99.32
 

 v0.99.30
 

 v0.99.29
 

 v0.99.29
 

 v0.99.29
 

 v0.99.27
 

 v0.99.25
 

 v0.99.23
 

 v0.99.23
 

 v0.99.21
 

 v0.99.19
 

 v0.99.17
 

 v0.99.15
 

 v0.99.13
 

 v0.99.9
 

 v0.99.9
 

 v0.99.7
 

 v0.99.5
 

 v0.99.3
 

 v0.99.1
 

 v0.99.1
 

 v0.99.0
 

 v0.99.0
 

 Delete Bootcamp_octad_setup.R 

 Delete Bootcamp_octad_example.R 

 Update README.md 

 Update README.md 

 Update README.md 

 Paper link
 

 Example link
 

 stable 0.99
 

 Update octad.Rmd

edited rmd 

 Octad_99
 

 octad 0.99.0
 

 octad 0.99.0
 

 updated drugs rges

updated drugs rges
 

 Diff_Exp.R

Given
case_id and control_id from dz_expr counts df
parameters from set_parameters.R
runs DE using edgeR
 

 Updated Core functions and create dz sig

Updated Core functions and create dz sig
 

 Fixed some syntax errors

Fixed some syntax errors
 

 Fixed typo in contrast mutants

Fixed typo in contrast mutants results
 

 Fixed Merging issue from Mapping

-Replace merging issue from mapping w/ left_join via dplyr
-This prevents the issue of missing hits while merging

-added create_dz_signature_geneMut.R
script helps to calculate gene mutation vs. non-mutant tumor and normal tissue of a specified gene
 

 updated dir paths

workflow.R now requires directory to point to:
1. code folder (where all codes stored)
2. output folder (default folder for output)
3. data folder (folder required for loading raw data files to run code)

workflow will also create a subdirectory output folder for cancers ran. The subdir will have title : cancer_genemutant_dataran_methodused e.g glioma_idh1_180101_edgeR/
 

 compute all cancers
 

 for parameter optimization
 

 update
 

 add outlier removal option
 

 add drug hits visualization
 

 add drug hits evaluation and visualization
 

 reformat
 

 add cell line correlation
 

 update DS_store
 

 integrate
 

 Fixed counts return

Counts should set to normalized counts
 

 support inferred genes
 

 merge stages and relax thresholds
 

 Add files via upload

function to query GDC API via GENE & Project 

 add stage feature
 

 add batch pathway prediction two sides
 

 add batch pathway prediction two sides
 

 first
 

 first
 

 first
 

 0.41 partial responce to review
 

 0.17 partial responce to review
 

 vignettes chunk 21
 

 v3.3.13 - version bump
 

 fixed 3 printf calls
 

 Correct linking directory on linux
 

 Update R CMD check workflow
 

 Link to copied files
 

 Merge changes

Merge branch 'ucrt-precompiled' of https://github.com/grimbough/Rhdf5lib into ucrt-precompiled

# Conflicts:
#	src/Makevars.win
 

 Update NEWS
 

 Enclose path in quotes
 

 Simplify windows building script
 

 Merge remote-tracking branch 'bioc/master' into ucrt-precompiled
 

 Update job name
 

 Add ucrt-x64 library versions
 

 Add pkgdown logo
 

 refactor: remove paste in stop
 

 Update vignette to include instructions for shared hub location across multiple users
 

 Closes #31

  - add instructions for creating a shared hub across multiple users
 

 Update vignette with shared cache instructions
 

 Merge branch 'RELEASE_3_14'
 

 Updating version number in NEWS and correcting URL in DESCRIPTION
 

 trying to increment version to next allowed number - trying same as devel
 

 trying another time to increment version to next allowed number
 

 incrementing version to next allowed number (hopefully)
 

 resetting version to 1.37.0 to avoid illegal bump
 

 missing event on stypesHelp2
 

 minor reformating
 

 changed details box
 

 updated help
 

 updated help
 

 Help Section Update
 

 add missing dep 

 Merge branch 'main' of github.com:ETHZ-INS/scanMiRApp into main
 

 disable rnor7
 

 merge

Merge branch 'main' of github.com:ETHZ-INS/scanMiRApp into main

# Conflicts:
#	R/scanMiRAnno.R
 

 version bump
 

 remove useless package
 

 Merge pull request #8 from SPPearce:SPPearce

Fix makeTable when asking for one window 

 Update NEWS and DESCRIPTION; Bump version
 

 Move the simpler vignettes to READMEN
 

 Add 'plotFixationSites' and 'plotParallelSites'; add print function for 'alignment' object
 

 'biocthis' version 1.5.0 generated GHA
 

 Add warning about status of FeatureDb-releated functionalities
 

 Merge branch 'master' into token-timeout
 

 version bump and NEWS for avdata() / avdata_import()
 

 refactor avdata()

- use getWorkspace("workspace.attributes") rather than getAttributesTSV
- more carefully exclude non-'DATA' elements
 

 Make sure internal helper map_SQLtypes_to_Rtypes() handles enum types
 

 add new features to NEWS file and change date in DESCRIPTION
 

 fix bug in y labels in dimension reduction plots (use here y_coord)
 

 update measured missing tabs, missing means all values are missing
 

 update maxQuant function and allow also for txt file import
 

 Merge pull request #232 from rformassspectrometry/filterPrecursorMzValue

Add filterPrecursorMzValue to support filtering by multiple m/z values 

 refactor: add filterPrecursorMzRange and depracate filterPrecursorMz
 

 fix: address Sebastian's comments
 

 Bump version
 

 feat: add filterPrecursorMzValues (issue #230)

- Add the `filterPrecursorMzValues` method to enable filtering based on multiple
  target precursor m/z values.
 

 updating info in the README
 

 updating the news for 1.7.2
 

 updating citation info
 

 Updated news

 

 Increased the version number from 2.13.1 to 2.13.2 .
 

 Introduced the argument calc.miss=FALSE in h.forestPlot to avoid computing
summaries in traits.forest and types.forest functions unless the user wants
to calculate and fill all 3 summaries (e.g. Meta, 1-sided, 2-sided).
Also fixed minor bug in h.traits which was generating error when
traits.forest was calling h.traits with one SNP.
 

 Merge pull request #4 from functionalgenomics/Telesc_multiovbyaln_minOv

Updating Telescope minimum overlap and implementing approach for alignments overlapping multiple features 

 Version bump
 

 Decommented lines in test_TEtranscripts.R
 

 Decommented lines in test_TEtranscripts.R
 

 Merge pull request #3 from pablo-rodr-bio2/updateSparse

Update sparse functions. Optimizations on TEtranscripts and Telescope methods. 

 version Bump
 

 Added if for when minOverlap = 0 and no overlaps are included in 'no_features'
 

 Telescope change all rowSums2 and colSums2
 

 Modified Telescope.R so that only alignments mapping to features but where the overlap is < min Overlap are consiedered as no_feature counts
 

 TEtranscript new .ttEstep() and .ttMstep()
 

 TEtrasncripts reverting Qmat div, new cntvecovtx
 

 TEtranscripts new Qmat div and cntvecovtx creation
 

 TEtranscripts new buildOvAlignmentsMatrix
 

 changed github workflow
 

 version bump
 

 update news
 

 add mp_extract_taxatree and mp_extract_otutree, alias of mp_extract_tree
 

 Merge pull request #26 from Nanostring-Biostats/dev

Update master to dev 1.3.1 

 Update news
 

 Pull in bioc version bumps
 

 #24 fix typo
 

 Version Bump

 

 Fixed github issue 114 - Wrong position of chromosome names

A bug caused the names of the chromosomes to be plotted at the wrong position when the chromosomes  where unordered and a custom genome was used. 

 Removed debugging messages

 

 update reference inference
 

 inferSpecies add species meta info
 

 update to inferSpecies
 

 temporary fixes for spatialData deprecation
 

 Register 3 NCBI assemblies for Acyrthosiphon pisum
 

 fixes #109
 

 News update and version bump
 

 line indentations
 

 Added CRISPRai models
 

 Merge pull request #60 from jwokaty/fix-generateBiocPkgDOI-return

Return DOI or message, bump version 

 Improving vignette.
 

 added gsea type testing
 

 updated package with gsea type testing
 

 Select files more specifically
 

 Fixed indexing issue with steinbock graphs
 

 Code cleanup.
 

 Code cleanup.
 

 Switched to useEnsembl istead of useMart
 

 Update DESCRIPTION
 

 v1.6.0 update

1. Adjust the default mitochondrial filtering cutoff in GetCellMat()

2. Add a new feature to evaluate appropriate background cutoffs
 

 new build of igv.min.js (2.10.5) supporting zoomOut.  added width to getGenomicRegion
 

 uses, and adapts to, igv.js version 2.10.2
 

 Merge bug fixes from release
 

 plotPairsArches clip.noArches parameter
 

 fix hlaGDS2Geno()
 

 Fix BioC HiC test
 

 removing cache lock at import time if running on bioc build servers (workaround for weird bioc build failures)
 

 roll-up fixes: blacklist, parallel, spikein normalization, Called
 

 fix: fix BiocCheck warnings
 

 somehow KYCG.Rmd got deleted, add back
 

 Merge pull request #94 from rformassspectrometry/bioc_submission

refactor: address comments from @jianhong 

 sob panel/viewr
 

 ...
 

 Added grid package to dependencies to fix BioC build
 

 version
 

 version for release branch
 

 Minor code style changes
 

 Updated citation in README
 

 Improve test coverage
 

 Depend on rhdf5
 

 first implementation of metadata read/write
 

 Fix check_mod_order
 

 Preserve modality order
 

 version bump
 

 Merge remote-tracking branch 'upstream/master'
 

 Remove the RGtk2
 

 loadEData TCGA: fix cTD version
 

 getGenesets: new msigdb collections
 

 bump to 1.13.13, fix smaller continuous data bug. add f_min and n_min in dbStats
 

 vignettes update
 

 unload loaded namespaces
 

 version bump 1.31.27
 

 update test_checkForVersionNumberMismatch
 

 use tempfiles as package names
 

 remove double colons
 

 added bookdown to suggested packages
 

 rebuilt pkgdown site
 

 new HTML docs page: `import_small_molecule_protein_interactions`
 

 Bioc Workshop vignette: added point about small molecule interactions
 

 added `dontrun` to examples using `consensuspathdb_download` to avoid timeouts on bioc build servers
 

 The build was failing due to changes to StandardizedExperiment objects.
 

 Version bump
 

 Fixed logic for clipped arches
 

 annoDomains rectHic bug fix
 

 Merge pull request #83 from UW-GAC/sparsematrix_bug

bug fix: makeSparseMatrix handles numeric sample IDs 

 Merge pull request #81 from UW-GAC/github_actions

replace travis build with github actions 

 only run checks on linux
 

 replace travis build with github actions
 

 bump to 1.13.12, update to KYCG vignette
 

 before deleting getDatabaseSetOverlap
 

 fix to num_dtna