pneuvial/adjclust issues and pull requests

#82 - snpClust Problem while setting all > 1 to 1

Issue - State: closed - Opened by lisiarend 7 months ago - 3 comments

#81 - [macOS] `adjclust` 0.6.9 fails to build with Clang

Issue - State: closed - Opened by barracuda156 about 1 year ago - 24 comments

#80 - version 0.6.9

Pull Request - State: closed - Opened by tuxette about 1 year ago

#79 - Fix orcid in DESCRIPTION

Pull Request - State: closed - Opened by pneuvial about 1 year ago - 1 comment

#78 - OMP proper control

Pull Request - State: closed - Opened by tuxette about 1 year ago - 1 comment

#77 - version 0.6.8 solving CRAN issues

Pull Request - State: closed - Opened by tuxette about 1 year ago

#76 - plotSim: add an option to plot a band or check that the existing option works properly

Issue - State: open - Opened by tuxette about 1 year ago
Labels: enhancement

#75 - More than 2 OMP threads launched in examples, vignettes, and tests

Issue - State: closed - Opened by tuxette about 1 year ago - 2 comments
Labels: bug, enhancement

#74 - Unecessary verbose in plot

Issue - State: open - Opened by tuxette about 1 year ago
Labels: enhancement

#73 - Improved citation

Issue - State: closed - Opened by tuxette about 1 year ago - 1 comment
Labels: enhancement

#72 - Update plots in README

Issue - State: closed - Opened by pneuvial almost 2 years ago - 1 comment

#71 - release 0.6.7

Pull Request - State: closed - Opened by tuxette almost 2 years ago

#70 - fixed issue #30

Pull Request - State: closed - Opened by tuxette almost 2 years ago - 1 comment

#69 - Tentative fix for #68

Pull Request - State: closed - Opened by tuxette almost 2 years ago - 1 comment

#68 - [CRAN NOTE] C++ specification

Issue - State: closed - Opened by pneuvial almost 2 years ago - 3 comments

#67 - Test coverage

Pull Request - State: closed - Opened by pneuvial almost 2 years ago - 1 comment

#66 - updated citation to comply to new CRAN standards (fixed #62)

Pull Request - State: closed - Opened by tuxette almost 2 years ago

#65 - Why is appveyor still running?

Issue - State: closed - Opened by tuxette almost 2 years ago - 2 comments
Labels: bug

#64 - plotSim: 'h' might not be well interpreted for `dgCMatrix`

Issue - State: closed - Opened by tuxette almost 2 years ago - 1 comment
Labels: bug, enhancement

#63 - ggplot2 version of plotSim

Pull Request - State: closed - Opened by tuxette almost 2 years ago - 1 comment

#62 - update CITATION file

Issue - State: closed - Opened by tuxette almost 2 years ago - 1 comment
Labels: bug

#61 - Bug in NAMESPACE: need to import SnpMatrix

Issue - State: closed - Opened by pneuvial almost 2 years ago - 1 comment
Labels: bug

#60 - Increase test coverage

Issue - State: closed - Opened by pneuvial about 2 years ago - 2 comments

#59 - Why do we have cutree_chac instead of cutree.chac?

Issue - State: closed - Opened by pneuvial about 2 years ago - 1 comment
Labels: question

#58 - Fix #45 (update 'calls' for 'adjclust.*' methods)

Pull Request - State: closed - Opened by pneuvial about 2 years ago

#57 - Write an article to complement Guénard & Legendre JSS 2022

Issue - State: open - Opened by tuxette about 2 years ago
Labels: question

#56 - Update pkgdown gha

Pull Request - State: closed - Opened by pneuvial about 2 years ago

#55 - Fix pkgdown action

Issue - State: closed - Opened by pneuvial about 2 years ago

#54 - Fix issue #49

Pull Request - State: closed - Opened by pneuvial about 2 years ago

#53 - Classes 'chac' and 'hclust': inheritance needed?

Issue - State: closed - Opened by tuxette over 2 years ago - 2 comments
Labels: enhancement, question

#52 - added information about correction and subsequent message for select …

Pull Request - State: closed - Opened by tuxette over 2 years ago

#51 - clarified ward.D vs ward.D2 vs adjclust and updated references (fix #16)

Pull Request - State: closed - Opened by tuxette over 2 years ago - 1 comment
Labels: enhancement

#50 - When loading package in R, can not find the package sparseMatrixStats

Issue - State: closed - Opened by Ledolter almost 3 years ago - 1 comment

#49 - Tests should not use library("adjclust")

Issue - State: closed - Opened by pneuvial almost 3 years ago
Labels: enhancement

#48 - Fix BioC dependencies in GHA "R-CMD-check"

Issue - State: closed - Opened by pneuvial over 3 years ago - 1 comment

#47 - Increase speed, and reduce memory usage

Pull Request - State: closed - Opened by GabrielHoffman over 3 years ago - 13 comments

#46 - Faster version and a question

Issue - State: open - Opened by GabrielHoffman over 3 years ago - 5 comments

#45 - Entry 'call' of the output object is that of the internal function

Issue - State: closed - Opened by tuxette over 4 years ago - 3 comments
Labels: enhancement

#44 - check plotSim for small matrices

Issue - State: closed - Opened by tuxette about 5 years ago - 2 comments
Labels: bug

#43 - No more NA in toy examples from snpClust

Issue - State: closed - Opened by tuxette about 5 years ago
Labels: bug

#42 - Do we need snpClust.dgCMatrix?

Issue - State: closed - Opened by pneuvial over 5 years ago - 1 comment
Labels: enhancement

#41 - User-defined breaks in 'plotSim'

Issue - State: closed - Opened by pneuvial over 5 years ago - 2 comments
Labels: enhancement

#40 - change plotSim with ggplot2

Issue - State: closed - Opened by tuxette about 6 years ago - 10 comments
Labels: enhancement

#39 - describe the algorithm

Issue - State: closed - Opened by tuxette about 6 years ago - 1 comment
Labels: enhancement, wontfix

#38 - Diagonal elements in plotSim with dendrogram

Issue - State: closed - Opened by pneuvial over 6 years ago - 4 comments

#37 - Color scale and borders in plotSim heatmaps

Issue - State: closed - Opened by pneuvial over 6 years ago - 1 comment
Labels: enhancement

#36 - Node labels in plotSim

Issue - State: closed - Opened by pneuvial over 6 years ago - 1 comment
Labels: enhancement

#35 - output of ld is not symmetric ?

Issue - State: closed - Opened by tuxette over 6 years ago - 2 comments
Labels: enhancement

#34 - hclust/adjClust results comparison

Issue - State: closed - Opened by ghost over 6 years ago - 2 comments

#33 - nodeLabel to display the order of succesive mergings

Pull Request - State: closed - Opened by ghost over 6 years ago

#32 - Wrong labels in plot.chac

Issue - State: closed - Opened by pneuvial almost 7 years ago - 2 comments

#31 - Add option to label merges on dendrogram

Issue - State: closed - Opened by pneuvial almost 7 years ago - 4 comments

#30 - improved plotSim

Issue - State: closed - Opened by tuxette almost 7 years ago - 2 comments
Labels: enhancement

#29 - correct dissimilarity part of the vignette NotesCCAHC

Issue - State: closed - Opened by tuxette almost 7 years ago - 1 comment
Labels: enhancement

#28 - make test for new features

Issue - State: closed - Opened by tuxette almost 7 years ago - 1 comment
Labels: enhancement

#27 - implement model selection

Issue - State: closed - Opened by tuxette almost 7 years ago - 1 comment
Labels: enhancement

#26 - change the way arbitrary similarities are handled

Issue - State: closed - Opened by tuxette almost 7 years ago - 3 comments
Labels: enhancement, question

#25 - test_hicClust is slow

Issue - State: closed - Opened by pneuvial about 7 years ago - 2 comments
Labels: enhancement

#24 - Useless file src/registerDynamicSymbol.c ?

Issue - State: closed - Opened by pneuvial about 7 years ago - 2 comments
Labels: question

#23 - almost positive matrices

Issue - State: closed - Opened by tuxette about 7 years ago - 2 comments
Labels: question

#22 - snpStats

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: question

#21 - sparse matrices

Issue - State: closed - Opened by tuxette about 7 years ago - 4 comments
Labels: enhancement

#20 - Check all outputs of adjClust

Issue - State: closed - Opened by tuxette about 7 years ago
Labels: bug

#19 - Check validity of the various heights when using a similarity and with the different transformations

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: enhancement, question

#18 - Plots produced by tests

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: question

#17 - duplicated png files in docs/

Issue - State: closed - Opened by pneuvial about 7 years ago - 1 comment
Labels: enhancement

#16 - ward.D and ward.D2

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: enhancement

#15 - Cutree with decreasing merges

Issue - State: closed - Opened by tuxette about 7 years ago
Labels: enhancement

#14 - Add new tests

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: enhancement

#13 - Weird outputs in adjclust

Issue - State: closed - Opened by tuxette about 7 years ago - 1 comment
Labels: enhancement, question

#12 - hicClust does not allow input of class 'matrix'

Issue - State: closed - Opened by tuxette over 7 years ago
Labels: enhancement

#11 - diagonal equal to 1

Issue - State: closed - Opened by tuxette over 7 years ago - 1 comment
Labels: enhancement

#10 - improved plot

Issue - State: closed - Opened by tuxette over 7 years ago - 2 comments
Labels: enhancement

#9 - missing dataset

Issue - State: closed - Opened by tuxette over 7 years ago
Labels: bug

#8 - snpClust with maximum bandwidth

Issue - State: closed - Opened by tuxette over 7 years ago - 2 comments
Labels: enhancement

#7 - check if all functions in the package are used

Issue - State: closed - Opened by tuxette over 7 years ago - 1 comment
Labels: question

#6 - propose default values for h

Issue - State: closed - Opened by tuxette over 7 years ago

#5 - plot function

Issue - State: closed - Opened by pneuvial over 7 years ago - 2 comments

#4 - version 0.4.0

Pull Request - State: closed - Opened by rewee over 7 years ago - 1 comment

#3 - Non-positive 'gains' in adjclust

Issue - State: closed - Opened by pneuvial about 8 years ago - 3 comments
Labels: enhancement

#2 - Add test for reproducibility between flavors of adjClustBand

Issue - State: closed - Opened by pneuvial over 8 years ago - 1 comment

#1 - Add test for reproducibility wrt 'rioja'

Issue - State: closed - Opened by pneuvial over 8 years ago - 2 comments

GitHub / pneuvial/adjclust issues and pull requests