Function copied from ptolemy, for choosing a good initial set of colors for cell types
document colorcelltypes
add color info to vignettes
add colorCellTypes function to vignettes
fix iss165
vignette bugfix
copy test script for colorCellTypes from ptolemy
Updated the temp folder creation logic
updated package version
Hardcode isRelease to true and comment out to deploy to all envs
New include
add specs and remove @exports
add missing @params
R CMD check fixes
new documentation
Remove exports
Fix imports
Update to MIT license
Add to .Rbuildignore
complete docs
Fix documentation
Reference global variable for R CMD check
doc update
Change package name to InSituType
Change package name in Rcpp files
Linting style changes
Update documentation
Unify names for vignettes
delete settings file
Remove writing plot to file
Keep as one row matrix
Render latest vignettes
BiocCheck items
Revert "Remove writing plot to file"
Specify package for dataset
Specify package for data
Update vignettes with reference to CosMx
Bump version
SingleCellExperiment option for core functions
Add dependency
Use one core for building vignettes
Add documentation
keep supercluster consister when subclustering
subclustered cells are now required to fall within their original supercluster, even if another supercluster has a greater loglik
Bump to version 0.99.3
add link to manuscript and citation
update README
correct dependencies flowchart in readme
remove dependency on lsa package in DESCRIPTION; faster way to calculate cell-level cosine similarity with celltype profiles in get_anchor_stats function
Don't track RStudio project file
Remove set.seed usage
Bump version
Change maintainer
Add examples
Merged PR 15109: Update azure-pipelines.yml for Azure Pipelines
Related work items: #175413
Update azure-pipelines.yml for Azure Pipelines
Updated trigger
Removed 1.0 environments from main branch
Added QA 1.1 environment
Updated local path for copying
Fixed variable
Update azure-pipelines.yml for Azure Pipelines
Fixed globExpression
message help wip
sync with main
explicit convert to dgCMatrix for ensuring access to counts2@x in next line
Re-add writing plot to disk.
Implement OpenMP parallelization for lldist
Don't save plot
Added license
Fix merge error
Restore saving plot
Use 64 bit integers
filter anchor, platform adjustment
fix umap in flightpath
add utilities func
Bump version to 1.1.0
I add the updateReferenceProfiles function to estimate gene-level platform effect and rescale raw reference profile
update function name
replace the estimatePlatformEffects function with updated version
auto anchor selection & reference update
update estimatePlatformEffects function
update the name of output list
rename the output list name
anchor threshold, lost genes
anchor threshold
fix testthat
update mans
outlier beta range
lostgenes vs. blacklist
sparse array compatibility
net expr
default mc.cores option
handle glm error
fastglm method
remove warning_genes
fix 0 bg in Poisson start
fix zero bg in estimateBackground()
Remove unneeded dependency
Updated 13 files under /R
Updated 7 files under /src
Updated 32 files under /man
added protein insituType clustering
update InsituType.R
updated all files
testing folder updated
testing folder updated
InsituType function updated
Deleted rescale_reference.R
Updated gen_profiles_protein.R
Added gen_profiles_protein_old.R
Added 2 files to /data
Renamed default_signature_matrix.csv to human_signature_matrix.csv
Fix S4 method
Remove build outputs
Update docs
Deleted gen_profiles_protein_old.R
Updated nbclust.R
insitutype function updated for protein
gen_profiles_protein function updated
Add lsa as dependency
Add dependencies
update insitutypeML
update Rcpp functions
update lldist function
rcpp change
updated all files
Update pipeline for devnext.
updated chooseclusternumber for protein
Deleted NBClust-Plots
Deleted NBClust-Plots
added examples and commented lines
Add back ARMA fix
testing examples and tests files
Fix example and vignettes
Fix roxygen for Rcpp
Add dependencies
Deleted NBClust-Plots
Re-add dependencies
Fix errors in unit tests and examples
Fix example
Remove duplicates
calling signature matrix from the package
calling signature matrix from the package
updated vignette
updated the namespace
Deleted NBClust-Plots
Update version to 1.2.0
Update ado pipeline.
Merged PR 20275: Create "undefined" profile for cells with zero counts
Change behavior of InSituType in all modes--supervised, unsupervised, semi-supervised--to no longer error when there are cells with zero counts but instead set their cell type to "undefined".
For the other error in linked work item generate a more informative message indicating that the profiles do not have sufficient shared genes with panel.
Related work items: #201286
Bump version for dev branch
fix compatability with platform correction
add default and limit choices for assay_type
Bump dev version to v1.2.2
PD updates
update docs
update tests
update version and NEWS and README
code review updates
update news
delete duplicated functions
new docs
2nd code review updates
update FAQ - new qc recommendation
Merged PR 21765: handle collinearity issues with fastCohorting
handle collinearity issues with fastCohorting:
Reduce to 2 PC's.
If this fails, then try successively smaller # of cohorts with the 2 pc's.
Test with matching gene sets
Parallelize calls to lldist by profile
Determine number of cores for mclapply
saving flightpath plot to /tmp/NBClust-Plots/
better file naming with time formatting
file name without spaces
fixing 7X7 in for save size
typo fix for units
delete detritus in rescaleProfiles
iss161 update refineClusters
tidy vignettes
pass check()
make default settings more robust
and use lower max_iters in phase 1
update docs
partial progress
remove geosketch redundancy
and speed up subsampling
remove dependency on rcolorbrewer
delete comments
add colorCellTypes function
Function copied from ptolemy, for choosing a good initial set of colors for cell types
document colorcelltypes
add color info to vignettes
add colorCellTypes function to vignettes
fix iss165
vignette bugfix
copy test script for colorCellTypes from ptolemy
Updated the temp folder creation logic
updated package version
Hardcode isRelease to true and comment out to deploy to all envs
New include
add specs and remove @exports
add missing @params
R CMD check fixes
new documentation
Remove exports
Fix imports
Update to MIT license
Add to .Rbuildignore
complete docs
Fix documentation
Reference global variable for R CMD check
doc update
Change package name to InSituType
Change package name in Rcpp files
Linting style changes
Update documentation
Unify names for vignettes
delete settings file
Remove writing plot to file
Keep as one row matrix
Render latest vignettes
BiocCheck items
Revert "Remove writing plot to file"
Specify package for dataset
Specify package for data
Update vignettes with reference to CosMx
Bump version
SingleCellExperiment option for core functions
Add dependency
Use one core for building vignettes
Add documentation
keep supercluster consister when subclustering
subclustered cells are now required to fall within their original supercluster, even if another supercluster has a greater loglik
Bump to version 0.99.3
add link to manuscript and citation
update README
correct dependencies flowchart in readme
remove dependency on lsa package in DESCRIPTION; faster way to calculate cell-level cosine similarity with celltype profiles in get_anchor_stats function
Don't track RStudio project file
Remove set.seed usage
Bump version
Change maintainer
Add examples
Merged PR 15109: Update azure-pipelines.yml for Azure Pipelines
Related work items: #175413
Update azure-pipelines.yml for Azure Pipelines
Updated trigger
Removed 1.0 environments from main branch
Added QA 1.1 environment
Updated local path for copying
Fixed variable
Update azure-pipelines.yml for Azure Pipelines
Fixed globExpression
message help wip
sync with main
explicit convert to dgCMatrix for ensuring access to counts2@x in next line
Re-add writing plot to disk.
Implement OpenMP parallelization for lldist
Don't save plot
Added license
Fix merge error
Restore saving plot
Use 64 bit integers
filter anchor, platform adjustment
fix umap in flightpath
add utilities func
Bump version to 1.1.0
I add the updateReferenceProfiles function to estimate gene-level platform effect and rescale raw reference profile
update function name
replace the estimatePlatformEffects function with updated version
auto anchor selection & reference update
update estimatePlatformEffects function
update the name of output list
rename the output list name
anchor threshold, lost genes
anchor threshold
fix testthat
update mans
outlier beta range
lostgenes vs. blacklist
sparse array compatibility
net expr
default mc.cores option
handle glm error
fastglm method
remove warning_genes
fix 0 bg in Poisson start
fix zero bg in estimateBackground()
Remove unneeded dependency
Updated 13 files under /R
Updated 7 files under /src
Updated 32 files under /man
added protein insituType clustering
update InsituType.R
updated all files
testing folder updated
testing folder updated
InsituType function updated
Deleted rescale_reference.R
Updated gen_profiles_protein.R
Added gen_profiles_protein_old.R
Added 2 files to /data
Renamed default_signature_matrix.csv to human_signature_matrix.csv
Fix S4 method
Remove build outputs
Update docs
Deleted gen_profiles_protein_old.R
Updated nbclust.R
insitutype function updated for protein
gen_profiles_protein function updated
Add lsa as dependency
Add dependencies
update insitutypeML
update Rcpp functions
update lldist function
rcpp change
updated all files
Update pipeline for devnext.
updated chooseclusternumber for protein
Deleted NBClust-Plots
Deleted NBClust-Plots
added examples and commented lines
Add back ARMA fix
testing examples and tests files
Fix example and vignettes
Fix roxygen for Rcpp
Add dependencies
Deleted NBClust-Plots
Re-add dependencies
Fix errors in unit tests and examples
Fix example
Remove duplicates
calling signature matrix from the package
calling signature matrix from the package
updated vignette
updated the namespace
Deleted NBClust-Plots
Update version to 1.2.0
Update ado pipeline.
Merged PR 20275: Create "undefined" profile for cells with zero counts
Change behavior of InSituType in all modes--supervised, unsupervised, semi-supervised--to no longer error when there are cells with zero counts but instead set their cell type to "undefined".
For the other error in linked work item generate a more informative message indicating that the profiles do not have sufficient shared genes with panel.
Related work items: #201286
Bump version for dev branch
fix compatability with platform correction
add default and limit choices for assay_type
Bump dev version to v1.2.2
PD updates
update docs
update tests
update version and NEWS and README
code review updates
update news
delete duplicated functions
new docs
2nd code review updates
update FAQ - new qc recommendation
Merged PR 21765: handle collinearity issues with fastCohorting
handle collinearity issues with fastCohorting:
Related work items: #211163
Bump version for dev to 1.2.3
bugfix
rownames(sds) was creating an error in rna mode.
Update pipeline for dev branch.
Related work items: #211130
faqs update
updates per LW code review
vignette finessing
r cmd check updates
faq updates
remove vestigial plots