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
greenelab/ADAGEpath documentation built on Sept. 24, 2017, 2:35 a.m.