Package: DuoClustering2018 1.31.0

Angelo Duò

DuoClustering2018: Data, Clustering Results and Visualization Functions From Duò et al (2018)

Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.

Authors:Angelo Duò, Charlotte Soneson

DuoClustering2018_1.31.0.tar.gz
DuoClustering2018_1.31.0.tar.gz(r-4.7-any)DuoClustering2018_1.31.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DuoClustering2018/json (API)

# Install 'DuoClustering2018' in R:
install.packages('DuoClustering2018', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:DuoClustering2018-1.31.0(data/experiment 3.24)DuoClustering2018-1.30.0(data/experiment 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecelldataexperimentdatadatapkg

5.56 score 121 scripts 127 exports 73 dependencies

Last updated from:6894b97a36. Checks:1 ERROR, 2 NOTE, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR155
linux-develNOTE285
source / vignettesOK320
linux-releaseNOTE410

Exports:clustering_summary_filteredExpr10_Koh_v1clustering_summary_filteredExpr10_Koh_v2clustering_summary_filteredExpr10_KohTCC_v1clustering_summary_filteredExpr10_KohTCC_v2clustering_summary_filteredExpr10_Kumar_v1clustering_summary_filteredExpr10_Kumar_v2clustering_summary_filteredExpr10_KumarTCC_v1clustering_summary_filteredExpr10_KumarTCC_v2clustering_summary_filteredExpr10_SimKumar4easy_v1clustering_summary_filteredExpr10_SimKumar4easy_v2clustering_summary_filteredExpr10_SimKumar4hard_v1clustering_summary_filteredExpr10_SimKumar4hard_v2clustering_summary_filteredExpr10_SimKumar8hard_v1clustering_summary_filteredExpr10_SimKumar8hard_v2clustering_summary_filteredExpr10_Trapnell_v1clustering_summary_filteredExpr10_Trapnell_v2clustering_summary_filteredExpr10_TrapnellTCC_v1clustering_summary_filteredExpr10_TrapnellTCC_v2clustering_summary_filteredExpr10_Zhengmix4eq_v1clustering_summary_filteredExpr10_Zhengmix4eq_v2clustering_summary_filteredExpr10_Zhengmix4uneq_v1clustering_summary_filteredExpr10_Zhengmix4uneq_v2clustering_summary_filteredExpr10_Zhengmix8eq_v1clustering_summary_filteredExpr10_Zhengmix8eq_v2clustering_summary_filteredHVG10_Koh_v1clustering_summary_filteredHVG10_Koh_v2clustering_summary_filteredHVG10_KohTCC_v1clustering_summary_filteredHVG10_KohTCC_v2clustering_summary_filteredHVG10_Kumar_v1clustering_summary_filteredHVG10_Kumar_v2clustering_summary_filteredHVG10_KumarTCC_v1clustering_summary_filteredHVG10_KumarTCC_v2clustering_summary_filteredHVG10_SimKumar4easy_v1clustering_summary_filteredHVG10_SimKumar4easy_v2clustering_summary_filteredHVG10_SimKumar4hard_v1clustering_summary_filteredHVG10_SimKumar4hard_v2clustering_summary_filteredHVG10_SimKumar8hard_v1clustering_summary_filteredHVG10_SimKumar8hard_v2clustering_summary_filteredHVG10_Trapnell_v1clustering_summary_filteredHVG10_Trapnell_v2clustering_summary_filteredHVG10_TrapnellTCC_v1clustering_summary_filteredHVG10_TrapnellTCC_v2clustering_summary_filteredHVG10_Zhengmix4eq_v1clustering_summary_filteredHVG10_Zhengmix4eq_v2clustering_summary_filteredHVG10_Zhengmix4uneq_v1clustering_summary_filteredHVG10_Zhengmix4uneq_v2clustering_summary_filteredHVG10_Zhengmix8eq_v1clustering_summary_filteredHVG10_Zhengmix8eq_v2clustering_summary_filteredM3Drop10_Koh_v1clustering_summary_filteredM3Drop10_Koh_v2clustering_summary_filteredM3Drop10_KohTCC_v1clustering_summary_filteredM3Drop10_KohTCC_v2clustering_summary_filteredM3Drop10_Kumar_v1clustering_summary_filteredM3Drop10_Kumar_v2clustering_summary_filteredM3Drop10_KumarTCC_v1clustering_summary_filteredM3Drop10_KumarTCC_v2clustering_summary_filteredM3Drop10_SimKumar4easy_v1clustering_summary_filteredM3Drop10_SimKumar4easy_v2clustering_summary_filteredM3Drop10_SimKumar4hard_v1clustering_summary_filteredM3Drop10_SimKumar4hard_v2clustering_summary_filteredM3Drop10_SimKumar8hard_v1clustering_summary_filteredM3Drop10_SimKumar8hard_v2clustering_summary_filteredM3Drop10_Trapnell_v1clustering_summary_filteredM3Drop10_Trapnell_v2clustering_summary_filteredM3Drop10_TrapnellTCC_v1clustering_summary_filteredM3Drop10_TrapnellTCC_v2clustering_summary_filteredM3Drop10_Zhengmix4eq_v1clustering_summary_filteredM3Drop10_Zhengmix4eq_v2clustering_summary_filteredM3Drop10_Zhengmix4uneq_v1clustering_summary_filteredM3Drop10_Zhengmix4uneq_v2clustering_summary_filteredM3Drop10_Zhengmix8eq_v1clustering_summary_filteredM3Drop10_Zhengmix8eq_v2duo_clustering_all_parameter_settings_v1duo_clustering_all_parameter_settings_v2plot_entropyplot_k_diffplot_performanceplot_stabilityplot_timingsce_filteredExpr10_Kohsce_filteredExpr10_KohTCCsce_filteredExpr10_Kumarsce_filteredExpr10_KumarTCCsce_filteredExpr10_SimKumar4easysce_filteredExpr10_SimKumar4hardsce_filteredExpr10_SimKumar8hardsce_filteredExpr10_Trapnellsce_filteredExpr10_TrapnellTCCsce_filteredExpr10_Zhengmix4eqsce_filteredExpr10_Zhengmix4uneqsce_filteredExpr10_Zhengmix8eqsce_filteredHVG10_Kohsce_filteredHVG10_KohTCCsce_filteredHVG10_Kumarsce_filteredHVG10_KumarTCCsce_filteredHVG10_SimKumar4easysce_filteredHVG10_SimKumar4hardsce_filteredHVG10_SimKumar8hardsce_filteredHVG10_Trapnellsce_filteredHVG10_TrapnellTCCsce_filteredHVG10_Zhengmix4eqsce_filteredHVG10_Zhengmix4uneqsce_filteredHVG10_Zhengmix8eqsce_filteredM3Drop10_Kohsce_filteredM3Drop10_KohTCCsce_filteredM3Drop10_Kumarsce_filteredM3Drop10_KumarTCCsce_filteredM3Drop10_SimKumar4easysce_filteredM3Drop10_SimKumar4hardsce_filteredM3Drop10_SimKumar8hardsce_filteredM3Drop10_Trapnellsce_filteredM3Drop10_TrapnellTCCsce_filteredM3Drop10_Zhengmix4eqsce_filteredM3Drop10_Zhengmix4uneqsce_filteredM3Drop10_Zhengmix8eqsce_full_Kohsce_full_KohTCCsce_full_Kumarsce_full_KumarTCCsce_full_SimKumar4easysce_full_SimKumar4hardsce_full_SimKumar8hardsce_full_Trapnellsce_full_TrapnellTCCsce_full_Zhengmix4eqsce_full_Zhengmix4uneqsce_full_Zhengmix8eq

Dependencies:AnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrExperimentHubfarverfastmapfilelockgenericsggplot2ggthemesgluegridExtragtablehttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglifecyclemagrittrmclustmemoisemimeopensslpillarpkgconfigplyrpngpurrrR6rappdirsRColorBrewerRcppreshape2rlangRSQLiteS4VectorsS7scalesSeqinfostringistringrsystibbletidyrtidyselectutf8vctrsviridisviridisLitewithrXVectoryaml

Plot performance summaries
Introduction | Load the necessary packages | Retrieve a data set | Read a set of clustering results | Define consistent method colors | Plot | Performance | Stability | Entropy | Timing | Differences in k | Session info | References
Rendered fromplot_performance.Rmdusingknitr::rmarkdown

Last update: 2020-10-21
Started: 2018-07-14

Apply clustering method
Introduction | Applying a new clustering algorithm to a provided data set | Session info | References
Rendered fromrun_clustering.Rmdusingknitr::rmarkdown

Last update: 2018-08-27
Started: 2018-07-14

Visualize data sets and clustering results with iSEE
Introduction | Load the necessary packages | Retrieve a data set | Read a set of clustering results | Merge data and clustering results | Visualize with iSEE | Session info | References
Rendered fromcombine_data_clustering.Rmdusingknitr::rmarkdown

Last update: 2018-08-27
Started: 2018-07-29

Readme and manuals

Help Manual

Help pageTopics
Help function for computing ARIari_df
Clustering summariesclustering_summary_filteredExpr10_KohTCC_v1 clustering_summary_filteredExpr10_Koh_v1 clustering_summary_filteredExpr10_KumarTCC_v1 clustering_summary_filteredExpr10_Kumar_v1 clustering_summary_filteredExpr10_SimKumar4easy_v1 clustering_summary_filteredExpr10_SimKumar4hard_v1 clustering_summary_filteredExpr10_SimKumar8hard_v1 clustering_summary_filteredExpr10_TrapnellTCC_v1 clustering_summary_filteredExpr10_Trapnell_v1 clustering_summary_filteredExpr10_Zhengmix4eq_v1 clustering_summary_filteredExpr10_Zhengmix4uneq_v1 clustering_summary_filteredExpr10_Zhengmix8eq_v1 clustering_summary_filteredHVG10_KohTCC_v1 clustering_summary_filteredHVG10_Koh_v1 clustering_summary_filteredHVG10_KumarTCC_v1 clustering_summary_filteredHVG10_Kumar_v1 clustering_summary_filteredHVG10_SimKumar4easy_v1 clustering_summary_filteredHVG10_SimKumar4hard_v1 clustering_summary_filteredHVG10_SimKumar8hard_v1 clustering_summary_filteredHVG10_TrapnellTCC_v1 clustering_summary_filteredHVG10_Trapnell_v1 clustering_summary_filteredHVG10_Zhengmix4eq_v1 clustering_summary_filteredHVG10_Zhengmix4uneq_v1 clustering_summary_filteredHVG10_Zhengmix8eq_v1 clustering_summary_filteredM3Drop10_KohTCC_v1 clustering_summary_filteredM3Drop10_Koh_v1 clustering_summary_filteredM3Drop10_KumarTCC_v1 clustering_summary_filteredM3Drop10_Kumar_v1 clustering_summary_filteredM3Drop10_SimKumar4easy_v1 clustering_summary_filteredM3Drop10_SimKumar4hard_v1 clustering_summary_filteredM3Drop10_SimKumar8hard_v1 clustering_summary_filteredM3Drop10_TrapnellTCC_v1 clustering_summary_filteredM3Drop10_Trapnell_v1 clustering_summary_filteredM3Drop10_Zhengmix4eq_v1 clustering_summary_filteredM3Drop10_Zhengmix4uneq_v1 clustering_summary_filteredM3Drop10_Zhengmix8eq_v1
Clustering summariesclustering_summary_filteredExpr10_KohTCC_v2 clustering_summary_filteredExpr10_Koh_v2 clustering_summary_filteredExpr10_KumarTCC_v2 clustering_summary_filteredExpr10_Kumar_v2 clustering_summary_filteredExpr10_SimKumar4easy_v2 clustering_summary_filteredExpr10_SimKumar4hard_v2 clustering_summary_filteredExpr10_SimKumar8hard_v2 clustering_summary_filteredExpr10_TrapnellTCC_v2 clustering_summary_filteredExpr10_Trapnell_v2 clustering_summary_filteredExpr10_Zhengmix4eq_v2 clustering_summary_filteredExpr10_Zhengmix4uneq_v2 clustering_summary_filteredExpr10_Zhengmix8eq_v2 clustering_summary_filteredHVG10_KohTCC_v2 clustering_summary_filteredHVG10_Koh_v2 clustering_summary_filteredHVG10_KumarTCC_v2 clustering_summary_filteredHVG10_Kumar_v2 clustering_summary_filteredHVG10_SimKumar4easy_v2 clustering_summary_filteredHVG10_SimKumar4hard_v2 clustering_summary_filteredHVG10_SimKumar8hard_v2 clustering_summary_filteredHVG10_TrapnellTCC_v2 clustering_summary_filteredHVG10_Trapnell_v2 clustering_summary_filteredHVG10_Zhengmix4eq_v2 clustering_summary_filteredHVG10_Zhengmix4uneq_v2 clustering_summary_filteredHVG10_Zhengmix8eq_v2 clustering_summary_filteredM3Drop10_KohTCC_v2 clustering_summary_filteredM3Drop10_Koh_v2 clustering_summary_filteredM3Drop10_KumarTCC_v2 clustering_summary_filteredM3Drop10_Kumar_v2 clustering_summary_filteredM3Drop10_SimKumar4easy_v2 clustering_summary_filteredM3Drop10_SimKumar4hard_v2 clustering_summary_filteredM3Drop10_SimKumar8hard_v2 clustering_summary_filteredM3Drop10_TrapnellTCC_v2 clustering_summary_filteredM3Drop10_Trapnell_v2 clustering_summary_filteredM3Drop10_Zhengmix4eq_v2 clustering_summary_filteredM3Drop10_Zhengmix4uneq_v2 clustering_summary_filteredM3Drop10_Zhengmix8eq_v2
Hyperparameter valuesduo_clustering_all_parameter_settings_v1
Hyperparameter valuesduo_clustering_all_parameter_settings_v2
DuoClustering2018DuoClustering2018
Plot entropy of cluster assignmentsplot_entropy
Plot differences between optimal, estimated and true number of clustersplot_k_diff
Plot performance of clustering methodsplot_performance
Plot stability of methodsplot_stability
Plot timing of methodsplot_timing
Koh data setssce_filteredExpr10_Koh sce_filteredExpr10_KohTCC sce_filteredHVG10_Koh sce_filteredHVG10_KohTCC sce_filteredM3Drop10_Koh sce_filteredM3Drop10_KohTCC sce_full_Koh sce_full_KohTCC
Kumar data setssce_filteredExpr10_Kumar sce_filteredExpr10_KumarTCC sce_filteredHVG10_Kumar sce_filteredHVG10_KumarTCC sce_filteredM3Drop10_Kumar sce_filteredM3Drop10_KumarTCC sce_full_Kumar sce_full_KumarTCC
SimKumar data setssce_filteredExpr10_SimKumar4easy sce_filteredExpr10_SimKumar4hard sce_filteredExpr10_SimKumar8hard sce_filteredHVG10_SimKumar4easy sce_filteredHVG10_SimKumar4hard sce_filteredHVG10_SimKumar8hard sce_filteredM3Drop10_SimKumar4easy sce_filteredM3Drop10_SimKumar4hard sce_filteredM3Drop10_SimKumar8hard sce_full_SimKumar4easy sce_full_SimKumar4hard sce_full_SimKumar8hard
Trapnell data setssce_filteredExpr10_Trapnell sce_filteredExpr10_TrapnellTCC sce_filteredHVG10_Trapnell sce_filteredHVG10_TrapnellTCC sce_filteredM3Drop10_Trapnell sce_filteredM3Drop10_TrapnellTCC sce_full_Trapnell sce_full_TrapnellTCC
Zheng data setssce_filteredExpr10_Zhengmix4eq sce_filteredExpr10_Zhengmix4uneq sce_filteredExpr10_Zhengmix8eq sce_filteredHVG10_Zhengmix4eq sce_filteredHVG10_Zhengmix4uneq sce_filteredHVG10_Zhengmix8eq sce_filteredM3Drop10_Zhengmix4eq sce_filteredM3Drop10_Zhengmix4uneq sce_filteredM3Drop10_Zhengmix8eq sce_full_Zhengmix4eq sce_full_Zhengmix4uneq sce_full_Zhengmix8eq
Calculate Shannon entropyshannon_entropy