Files in kkdey/aRchaic.site

Visualization, Exploration and Clustering of Ancient vs Modern BAM mutation patterns

.DS_Store

.RData

.Rbuildignore

.Rhistory

.Rprofile

.gitignore

DESCRIPTION

NAMESPACE

R/aRchaic_class.R R/aRchaic_class_beta.R R/aRchaic_cluster.R R/aRchaic_cluster_beta.R R/aRchaic_cluster_beta_mutation.R R/aRchaic_cluster_beta_mutation_flank.R R/aRchaic_cluster_beta_mutation_flank_pos.R R/aRchaic_cluster_beta_mutation_pos.R R/aRchaic_cluster_beta_pos.R R/aRchaic_cluster_beta_wo_strand.R R/aRchaic_cluster_beta_wo_strand_break.R R/aRchaic_mutation_trend.R R/aRchaic_pca.R R/aRchaic_pca_beta.R R/aRchaic_pool.R R/aRchaic_tsne.R R/aRchaic_tsne_beta.R R/aRchaic_view.R R/aggregate_signature_counts.R R/club_signature_counts.R R/damageLogo_1.R R/damageLogo_2.R R/damageLogo_3.R R/damageLogo_4.R R/damageLogo_5.R R/filter_by_mutation.R R/filter_by_mutation_flank.R R/filter_by_mutation_flank_pos.R R/filter_by_mutation_pos.R R/filter_by_pos.R R/filter_by_pos_pattern.R R/filter_out_strand.R R/filter_out_strand_break.R R/filter_signatures_only_location.R R/flanking_base_composition.R R/read_length_distribution.R R/strand_breaks_composition.R R/structureggplot_2.R R/theta_breakdown.R README.md

aRchaic.site.Rproj

articles/.DS_Store

articles/Bone2.jpg

articles/Bone3.png

articles/Bone4.png

articles/GitHub-Mark-64px.png

articles/GitHub-Mark.zip

articles/GitHub-Mark/.DS_Store

articles/GitHub-Mark/PNG/.DS_Store

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articles/GitHub-Mark/PNG/GitHub-Mark-32px.png

articles/GitHub-Mark/PNG/GitHub-Mark-Light-120px-plus.png

articles/GitHub-Mark/PNG/GitHub-Mark-Light-32px.png

articles/GitHub-Mark/PNG/GitHub-Mark-Light-64px.png

articles/GitHub-Mark/Vector/GitHub-Mark.ai

articles/GitHub-Mark/Vector/GitHub-Mark.eps

articles/archaic_plot.png

articles/bone.png

articles/demo.png

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articles/logos_with_text.key

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articles/logos_with_text/logos_with_text.003.png

articles/logos_with_text/logos_with_text.004.png

articles/mutation_trend_plot.png

articles/overview.png

articles/readlength_plot.png

articles/skoglund_plot.png

articles/skull.jpg

articles/skull.png

articles/trash

docs/.DS_Store

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docs/authors.html

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docs/output/.DS_Store

docs/output/README.md

docs/output/aRchaic_cluster.key

docs/output/aRchaic_cluster/aRchaic_cluster.001.png

docs/output/aRchaic_cluster/aRchaic_cluster.002.png

docs/output/aRchaic_cluster/aRchaic_cluster.003.png

docs/output/base_probs_temp_2.rda

docs/output/logo.png

docs/output/logo_Gok4_Skoglund.png

docs/output/logo_Gok4_Skoglund_2.png

docs/output/read_length.png

docs/output/skoglund_2/logo_clus_1.png

docs/output/skoglund_2/logo_clus_2.png

docs/output/skoglund_2/model.rda

docs/output/skoglund_2/structure.png

docs/output/skoglund_moderns_2/.DS_Store

docs/output/skoglund_moderns_2/logo_clus_1.png

docs/output/skoglund_moderns_2/logo_clus_2.png

docs/output/skoglund_moderns_2/model.rda

docs/output/skoglund_moderns_2/structure.png

docs/output/skoglund_moderns_2_background/logo_clus_1.png

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docs/output/skoglund_moderns_2_background/model.rda

docs/output/skoglund_moderns_2_background/pca.png

docs/output/skoglund_moderns_2_background/pca.rda

docs/output/skoglund_moderns_2_background/structure.png

docs/pkgdown.css

docs/pkgdown.js

docs/reference/aggregate_signature_counts.html

docs/reference/club_signature_counts.html

docs/reference/damageLogo_five.html

docs/reference/index.html

docs/reference/read_length_distribution.html

docs/skeleton.svg

docs/skull.svg

docs/stylesheets/bootstrap.2.2.2.min.css

docs/stylesheets/broman2.css

docs/stylesheets/kbroman.css

docs/stylesheets/print.css

docs/stylesheets/pygment_trac.css

docs/stylesheets/stylesheet.css

docs/test.html

docs/test.md

docs/tutorial.html

docs/vignettes.html

man/aggregate_signature_counts.Rd man/club_signature_counts.Rd man/damageLogo_five.Rd man/read_length_distribution.Rd

output/.DS_Store

output/README.md

output/aRchaic_cluster.key

output/aRchaic_cluster/aRchaic_cluster.001.png

output/aRchaic_cluster/aRchaic_cluster.002.png

output/aRchaic_cluster/aRchaic_cluster.003.png

output/base_probs_temp_2.rda

output/logo.png

output/logo_Gok4_Skoglund.png

output/logo_Gok4_Skoglund_2.png

output/read_length.png

output/skoglund_2/logo_clus_1.png

output/skoglund_2/logo_clus_2.png

output/skoglund_2/model.rda

output/skoglund_2/structure.png

output/skoglund_moderns_2/.DS_Store

output/skoglund_moderns_2/logo_clus_1.png

output/skoglund_moderns_2/logo_clus_2.png

output/skoglund_moderns_2/model.rda

output/skoglund_moderns_2/structure.png

output/skoglund_moderns_2_background/logo_clus_1.png

output/skoglund_moderns_2_background/logo_clus_2.png

output/skoglund_moderns_2_background/model.rda

output/skoglund_moderns_2_background/pca.png

output/skoglund_moderns_2_background/pca.rda

output/skoglund_moderns_2_background/structure.png

packrat/.DS_Store

packrat/init.R

packrat/packrat.lock

packrat/packrat.opts

packrat/src/R6/R6_2.2.0.tar.gz

packrat/src/Rcpp/Rcpp_0.12.9.tar.gz

packrat/src/assertthat/assertthat_0.1.tar.gz

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packrat/src/curl/curl_2.3.tar.gz

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packrat/src/devtools/devtools_1.12.0.tar.gz

packrat/src/digest/digest_0.6.12.tar.gz

packrat/src/evaluate/evaluate_0.10.tar.gz

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packrat/src/rstudioapi/rstudioapi_0.6.tar.gz

packrat/src/stringi/stringi_1.1.2.tar.gz

packrat/src/stringr/stringr_1.2.0.tar.gz

packrat/src/whisker/whisker_0.3-2.tar.gz

packrat/src/withr/withr_1.0.2.tar.gz

kkdey/aRchaic.site documentation built on May 20, 2019, 10:31 a.m.