Files in greenelab/ADAGEpath
ADAGE-based Signature Analysis
.Rbuildignore
.gitignore
ADAGEpath.Rproj
DESCRIPTION
LICENSE
NAMESPACE
R/ADAGEpath.R
R/annotate_signature.R
R/cal_activity.R
R/data.R
R/geneset_activity.R
R/load_data.R
R/marginal_activity.R
R/process_signature.R
R/query_ArrayExpress.R
R/test_activation.R
R/visualize_network.R
README.md
data-raw/PAO1orthologs.R
data-raw/Pseudomonas_aeruginosa_PAO1.gene_info.gz
data-raw/build_compendium.R
data-raw/eADAGEmodel.R
data-raw/geneinfo.R
data-raw/net300_100models_1_100_k=300_seed=123_ClusterByweighted_avgweight_network_ADAGE.txt
data-raw/operons.R
data/PAO1orthologs.rda
data/PAcompendium.rda
data/eADAGEmodel.rda
data/experimentID.rda
data/geneinfo.rda
data/operons.rda
data/probedistribution.rda
inst/extdata/anr/WT1_(Pae_G1a).CEL
inst/extdata/anr/WT2_(Pae_G1a).CEL
inst/extdata/anr/WT3_(Pae_G1a).CEL
inst/extdata/anr/anr1_(Pae_G1a)_2.CEL
inst/extdata/anr/anr2_(Pae_G1a).CEL
inst/extdata/anr/anr3_(Pae_G1a).CEL
man/ADAGEpath.Rd
man/PAO1orthologs.Rd
man/PAcompendium.Rd
man/TDM_RNAseq.Rd
man/annotate_genes_in_signatures.Rd
man/annotate_shared_signatures.Rd
man/annotate_signatures_with_genesets.Rd
man/build_gene_geneset_map.Rd
man/build_limma.Rd
man/build_signature_overlap_matrix.Rd
man/calculate_activity.Rd
man/calculate_marginal_activity.Rd
man/check_accession.Rd
man/check_input.Rd
man/combine_geneset_outputs.Rd
man/download_raw.Rd
man/eADAGEmodel.Rd
man/enrich_test.Rd
man/experimentID.Rd
man/extract_signatures.Rd
man/fetch_geneset.Rd
man/find_associated_signatures.Rd
man/geneinfo.Rd
man/get_active_signatures.Rd
man/get_paretofront.Rd
man/get_sample_info.Rd
man/impute_miss_values.Rd
man/load_dataset.Rd
man/map_value_to_color.Rd
man/match_IDs.Rd
man/one_signature.Rd
man/one_signature_activity.Rd
man/operons.Rd
man/plot_activity_heatmap.Rd
man/plot_marginal_activation.Rd
man/plot_signature_overlap.Rd
man/plot_volcano.Rd
man/prepare_marginal_matrix.Rd
man/probedistribution.Rd
man/process_celfiles.Rd
man/quantile_norm.Rd
man/remove_redundant_signatures.Rd
man/signature_geneset_activity.Rd
man/test_signature_overlap.Rd
man/to_LocusTag.Rd
man/to_symbol.Rd
man/visualize_gene_network.Rd
man/zeroone_norm.Rd
vignettes/ArrayExpress-example.Rmd
vignettes/Factorial-design-example.Rmd
vignettes/RNAseq-example.Rmd
vignettes/Time-course-example.Rmd
vignettes/User-input-example.Rmd
