Files in kendomaniac/SCAtutorial

Supporting material for the manuscript Sparsely-Connected Autoencoder (SCA) for single cell RNAseq data mining

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

R/installing.rcasc.R README.md

SCAtutorial.Rproj

_pkgdown.yml

docs/.DS_Store

docs/404.html

docs/articles/.DS_Store

docs/articles/SCAvignette.html

docs/articles/SCAvignette_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/img/5clusters.png

docs/articles/img/is.png

docs/articles/img/learning.png

docs/articles/img/qcm-qcf.png

docs/articles/img/rCASC.png

docs/articles/img/scaworkflow.png

docs/articles/img/vsca.png

docs/articles/index.html

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/index.html

docs/reference/installing.rcasc.html

man/installing.rcasc.Rd

vignettes/.DS_Store

vignettes/.Rhistory

vignettes/SCAvignette.Rmd

vignettes/img/.DS_Store

vignettes/img/5clusters.png

vignettes/img/is.png

vignettes/img/learning.png

vignettes/img/qcm-qcf.png

vignettes/img/rCASC.png

vignettes/img/sca.png

vignettes/img/scaworkflow.png

vignettes/img/vsca.png

vignettes/scratch/.DS_Store

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/5

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/cluster.txt

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/freqMatrix.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/freqMatrix_clustering.output.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/markers.txt

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/pair_tp_tn_1

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/pair_tp_tn_2

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/pair_tp_tn_3

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/pair_tp_tn_4

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/pair_tp_tn_5

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/sing_tp_tn_1

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/sing_tp_tn_2

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/sing_tp_tn_3

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/sing_tp_tn_4

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/output_pickles/sing_tp_tn_5

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_1_pair_final_ranking.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_1_pair_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_1_singleton_all_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_1_singleton_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_1_singleton_positive_markers_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_2_pair_final_ranking.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_2_pair_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_2_singleton_all_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_2_singleton_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_2_singleton_positive_markers_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_3_pair_final_ranking.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_3_pair_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_3_singleton_all_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_3_singleton_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_3_singleton_positive_markers_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_4_pair_final_ranking.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_4_pair_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_4_singleton_all_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_4_singleton_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_4_singleton_positive_markers_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_5_pair_final_ranking.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_5_pair_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_5_singleton_all_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_5_singleton_full_unranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputdata/cluster_5_singleton_positive_markers_ranked.csv

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputmetadata.txt

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_discrete_pairs/rank 1.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_discrete_pairs/rank 40.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_discrete_pairs/rank 41.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_1.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_12.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_13.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_14.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_15.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_17.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_18.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_19.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_2.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_20.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_21.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_22.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_23.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_24.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_25.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_28.png

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vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_32.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_33.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_34.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_35.png

vignettes/scratch/Sun-Sep--6-04-34-52-2020/freqMatrix/5/outputvis/cluster_1_pairs_as_singletons/rank_36.png

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vignettes/setA/Results/setATF_GRIPH/5/outputvis/cluster_5_singleton_TP_TN.png

vignettes/setA/Results/setATF_GRIPH/5/outputvis/cluster_5pair_TP_TN.png

vignettes/setA/Results/setATF_GRIPH/5/permutation/0clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/0clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/0denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/0tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/1clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/1clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/1denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/1tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/2clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/2clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/2denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/2tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/3clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/3clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/3denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/3tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/4clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/4clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/4denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/4tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/5clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/5clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/5denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/5tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/6clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/6clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/6denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/6tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/7clustering.pdf vignettes/setA/Results/setATF_GRIPH/5/permutation/7clusteringGRIPH.pdf

vignettes/setA/Results/setATF_GRIPH/5/permutation/7denseSpace.csv

vignettes/setA/Results/setATF_GRIPH/5/permutation/7tSne.csv

vignettes/setA/Results/setATF_GRIPH/5/pvalMatrix.csv

vignettes/setA/Results/setATF_GRIPH/5/rawFeatureSelection.csv

vignettes/setA/Results/setATF_GRIPH/5/run.info

vignettes/setA/Results/setATF_GRIPH/5/setA_StabilitySignificativity.pdf vignettes/setA/Results/setATF_GRIPH/5/setA_StabilitySignificativityJittered.pdf

vignettes/setA/Results/setATF_GRIPH/5/setA_clustering.output.csv

vignettes/setA/Results/setATF_GRIPH/5/setA_score.csv

vignettes/setA/Results/setATF_GRIPH/5/setA_scoreSum.csv

vignettes/setA/Results/setATF_GRIPH/5/setA_scoreSumUNBIAS.csv

vignettes/setA/Results/setATF_GRIPH/5/setA_scoreUNBIAS.csv

vignettes/setA/Results/setATF_GRIPH/5/setA_stabilityPlot.pdf vignettes/setA/Results/setATF_GRIPH/5/setA_stabilityPlotUNBIAS.pdf

vignettes/setA/Results/setATF_GRIPH/ExitStatusFile

vignettes/setA/Results/setATF_GRIPH/containers.txt

vignettes/setA/Results/setATF_GRIPH/e202dc27581c.log

vignettes/setA/Results/setATF_GRIPH/run.info

vignettes/setA/Results/setATF_GRIPH/setA.csv

vignettes/setA/a2238aa22e9a.log

vignettes/setA/cancer_related_immuno_signatures.csv

vignettes/setA/containers.txt

vignettes/setA/f71dff9f9ea3.log

vignettes/setA/kinase-specific_phosphorylation_sites.csv

vignettes/setA/mirna.txt

vignettes/setA/mirnaTFISKinase.csv

vignettes/setA/run.info

vignettes/setA/setA.csv

vignettes/setA/setA_clustering.output.csv

vignettes/setA/tf.txt

kendomaniac/SCAtutorial documentation built on Sept. 11, 2020, 9:18 a.m.