Files in RGLab/HIPCMatrix
Microarray and RNA-seq Processing for ImmuneSpace
.Rbuildignore
.github/.gitignore
.github/pull_request_template.md
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
HIPCMatrix.Rproj
NAMESPACE
R/HMX.R
R/gene_set_enrichment_analysis.R
R/gene_sets.R
R/gene_symbol_mapping.R
R/hmx_differential_expression.R
R/hmx_feature_annotation.R
R/immune_response_predictor.R
R/make_raw_matrix.R
R/meta_data.R
R/normalize.R
R/prepare_files.R
R/runCreateMx.R
R/summarize.R
R/utils.R
README.md
data-raw/hgncAlias2Symbol.R
data-raw/meta_data_list.R
data-raw/update_hgnc_mapping.R
data/chaussabel_modules.rda
data/emory_blood_transcript_modules.rda
data/hgncAlias2Symbol.rda
data/hgncAlias2Symbol_version.rda
data/meta_data_list.rda
data/msigdb_immunologic_signatures.rda
data/orig_btm_list.rda
data/orig_chaussabel.rda
data/orig_emory.rda
data/orig_msigdb.rda
data/updated_btm_df.rda
data/updated_btm_list.rda
inst/CreateMatrixAssets/IlluminaManifests/HumanHT-12_V4_0_R2_15002873_B.bgx
inst/FeatureAnnotationSetDev/AffyPrimeView_2016.tsv
inst/FeatureAnnotationSetDev/Affy_HumanExonST_1_0_v2.R
inst/FeatureAnnotationSetDev/Affy_HumanExonST_1_0_v2.tsv
inst/FeatureAnnotationSetDev/Affy_HumanRSTAcustom.R
inst/FeatureAnnotationSetDev/Affy_HumanRSTAcustom.tsv
inst/FeatureAnnotationSetDev/Ensembl_86_GRCh38.tsv
inst/FeatureAnnotationSetDev/Ensembl_86_GRCh38_makeAnno.R
inst/FeatureAnnotationSetDev/GPL6883-11606.txt
inst/FeatureAnnotationSetDev/HEEBOHumanSetV1.R
inst/FeatureAnnotationSetDev/HEEBOHumanSetV1.tsv
inst/FeatureAnnotationSetDev/HEEBOHumanSetV1_unformatted.tsv
inst/FeatureAnnotationSetDev/HumanHT-12_V3_0_R3_11283641_A.txt
inst/FeatureAnnotationSetDev/HumanHT-12_V4_0_R2_15002873_B.txt
inst/FeatureAnnotationSetDev/HumanWG-6_V3_0_R3_11282955_A.txt
inst/FeatureAnnotationSetDev/IlluminaHumanHT-12_v3_2018.tsv
inst/FeatureAnnotationSetDev/IlluminaHumanHT-12_v4_2018.tsv
inst/FeatureAnnotationSetDev/IlluminaHumanRef8_v3_anno.tsv
inst/FeatureAnnotationSetDev/SDY1092_CustomAnno.R
inst/FeatureAnnotationSetDev/SDY1092_CustomAnno.tsv
inst/FeatureAnnotationSetDev/SDY1264_Trial1.tsv
inst/FeatureAnnotationSetDev/SDY1264_customAnno.tsv
inst/FeatureAnnotationSetDev/SDY1264_makeAnno.R
inst/FeatureAnnotationSetDev/SDY1289_makeAnno.R
inst/FeatureAnnotationSetDev/SDY1293_Control.tsv
inst/FeatureAnnotationSetDev/SDY1324_CustomAnno.tsv
inst/FeatureAnnotationSetDev/SDY1373_customAnno.tsv
inst/FeatureAnnotationSetDev/SDY1373_makeAnno.R
inst/FeatureAnnotationSetDev/SDY1630_CustomAnno.R
inst/FeatureAnnotationSetDev/SDY1630_CustomAnno.tsv
inst/FeatureAnnotationSetDev/SDY224_CustomAnno.tsv
inst/FeatureAnnotationSetDev/SDY224_makeAnno.R
inst/FeatureAnnotationSetDev/SDY300_CustomAnno.tsv
inst/FeatureAnnotationSetDev/SDY300_EXP13588_RNA_seq.703274.tsv
inst/FeatureAnnotationSetDev/SDY300_customAnno.R
inst/FeatureAnnotationSetDev/SDY787_customAnno.tsv
inst/FeatureAnnotationSetDev/SDY787_makeAnno.R
inst/FeatureAnnotationSetDev/SDY888_customAnno.tsv
inst/FeatureAnnotationSetDev/SDY888_makeAnno.R
inst/FeatureAnnotationSetDev/SDY903_customAnno.tsv
inst/FeatureAnnotationSetDev/SDY903_makeAnno.R
inst/FeatureAnnotationSetDev/hgu133plus2.tsv
inst/FeatureAnnotationSetDev/huex10stv2cdf.tar.gz
inst/FeatureAnnotationSetDev/hursta2a520709cdf.tar.gz
inst/FeatureAnnotationSetDev/illuminaHumanHT-12_v3_2018.R
inst/FeatureAnnotationSetDev/illuminaHumanHT-12_v4_2018.R
inst/FeatureAnnotationSetDev/illuminaHumanWG-6_v3.R
inst/FeatureAnnotationSetDev/unigene2symbol.tsv
inst/reports/immune_response_predictor.Rmd
inst/scripts/rerun-all.R
inst/scripts/rerun-matrix.R
inst/virtualStudyHelpers/CopyMatricesToVirtualSdy.R
inst/virtualStudyHelpers/addAnnoToVirtualSdy.R
man/HMX.Rd
man/chaussabel_modules.Rd
man/create_gene_alias_map.Rd
man/dot-fix_headers.Rd
man/dot-ge_list_to_flat_file.Rd
man/dot-getGEO_custom.Rd
man/dot-get_geo_supp_files.Rd
man/dot-get_supp_files_dir.Rd
man/dot-make_id_to_gsm_map.Rd
man/dot-map_feature_id_col.Rd
man/dot-map_sampleid_to_biosample_accession.Rd
man/dot-prep_geo_files.Rd
man/dot-prep_illumina_headers.Rd
man/dot-prep_immport_files.Rd
man/dot-process_affy.Rd
man/dot-process_illumina.Rd
man/dot-process_rna_seq.Rd
man/dot-process_two_color_array.Rd
man/dot-select_input_files.Rd
man/dot-subset_raw_illumina_dt.Rd
man/dot-write_raw_expression.Rd
man/emory_blood_transcript_modules.Rd
man/find_de_genes_eBayes.Rd
man/format_predictor_table.Rd
man/get_meta_data.Rd
man/gsea.Rd
man/hgncAlias2Symbol.Rd
man/hgncAlias2Symbol_version.Rd
man/makeAnnoDf.Rd
man/make_raw_matrix.Rd
man/mapAlias2Symbol.Rd
man/meta_data_list.Rd
man/msigdb_immunologic_signatures.Rd
man/normalize_matrix.Rd
man/normalize_microarray.Rd
man/normalize_rnaseq.Rd
man/orig_btm_list.Rd
man/orig_chaussabel.Rd
man/orig_emory.Rd
man/orig_msigdb.Rd
man/print.ImmuneResponsePredictor.Rd
man/retrieve_input_files.Rd
man/runCreateMx.Rd
man/summarize_by_gene_symbol.Rd
man/update_geneset_symbols.Rd
man/updated_btm_df.Rd
man/updated_btm_list.Rd
man/write_matrix.Rd
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/setup.R
tests/testthat/test-1-utils.R
tests/testthat/test-differential_expression.R
tests/testthat/test-gene_sets.R
tests/testthat/test-gene_symbol_mapping.R
tests/testthat/test-gsea.R
tests/testthat/test-irp.R
tests/testthat/test-make_raw_matrix.R
tests/testthat/test-metadata.R
tests/testthat/test-normalize.R
tests/testthat/test-prepare_files.R
tests/testthat/test-summarize.R
tests/testthat/test_data/affy_raw_mx.rds
tests/testthat/test_data/illumina_raw_mx.rds
tests/testthat/test_data/rna_raw_mx.rds
tests/testthat/test_data/sdy112/Ji_Batch2_11.295174.CEL
tests/testthat/test_data/sdy112/Ji_Batch2_12.295175.CEL
tests/testthat/test_data/sdy112/SDY112_gef.rds
tests/testthat/test_data/sdy1289/supp_files/Whole-blood_ARM4455/geo_soft_files/GSM343927.soft
tests/testthat/test_data/sdy1412/supp_files/Whole-blood_ARM4723/GSE123070_RAW.tar
tests/testthat/test_data/sdy1412/supp_files/Whole-blood_ARM4723/GSM3494581_RNA_P09_D0.count.txt.gz
tests/testthat/test_data/sdy1412/supp_files/Whole-blood_ARM4723/GSM3494630_RNA_P35_D3.count.txt.gz
tests/testthat/test_data/sdy1412/supp_files/Whole-blood_ARM4723/geo_soft_files/GSM3494581.soft
tests/testthat/test_data/sdy1412/supp_files/Whole-blood_ARM4723/geo_soft_files/GSM3494630.soft
tests/testthat/test_data/sdy1529/SDY1529_day0_gef.rds
tests/testthat/test_data/sdy1630/GSE133383_filtered_NKcounts_table.748979.csv
tests/testthat/test_data/sdy1630/SDY1630_gef.rds
tests/testthat/test_data/sdy180/supp_files/Whole-blood_ARM773/GSM744991.txt
tests/testthat/test_data/sdy180/supp_files/Whole-blood_ARM773/GSM744994.txt
tests/testthat/test_data/sdy180/supp_files/Whole-blood_ARM773/SDY180_raw_expression.txt
tests/testthat/test_data/sdy387/SDY387_EXP13732_microarray.703288.tsv
tests/testthat/test_data/sdy387/SDY387_gef.rds
tests/testthat/test_data/sdy640/supp_files/Whole-blood_ARM2863/GSE101710_Expression.raw.txt
tests/testthat/test_data/sdy640/supp_files/Whole-blood_ARM2863/GSE101710_RAW.tar
tests/testthat/test_data/sdy640/supp_files/Whole-blood_ARM2863/geo_soft_files/GSM2712880.soft
tests/testthat/test_data/sdy787/SDY787_gef.rds
tests/testthat/test_data/sdy787/supp_files/T-cell_ARM3144/GSE113891_PT_all_Count.tsv
tests/testthat/test_data/sdy787/supp_files/T-cell_ARM3144/GSE113891_PT_all_TPM.tsv.gz
tests/testthat/test_data/sdy787/supp_files/T-cell_ARM3144/geo_soft_files/GSM3122900.soft
