Files in CharlesJB/rnaseq
Wrapper Functions for RNA-Seq Post-Processing
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/DE.R
R/PCA.R
R/RUVg.R
R/batch_DE.R
R/batch_PCA.R
R/batch_volcanos.R
R/counts.R
R/data.R
R/deliverables.R
R/demo.R
R/format.R
R/import.R
R/odysse.R
R/parse_metadata.R
R/report.R
R/txi.R
R/volcano.R
README.md
data-raw/download_and_clean_ERCC92.sh
data-raw/download_and_clean_ensembl_btaurus.sh
data-raw/download_and_clean_ensembl_hsapiens.sh
data-raw/download_and_clean_ensembl_mmulata.sh
data-raw/download_and_clean_ensembl_mmusculus.sh
data-raw/download_and_clean_ensembl_rnorvegicus_5.0.sh
data-raw/download_and_clean_ensembl_rnorvegicus_6.0.sh
data-raw/download_and_clean_gencode_hsapiens.sh
data-raw/scripts/add_refseq.R
data-raw/scripts/format_ERCC92.R
data-raw/scripts/prepare_anno_ensembl.R
data-raw/scripts/prepare_anno_ensembl_fasta.R
data-raw/scripts/prepare_anno_ensembl_hsapiens.R
data-raw/scripts/prepare_anno_ensembl_old.R
data-raw/scripts/prepare_anno_gencode_hsapiens.R
data/ERCC92.RData
inst/extdata/de_infos.csv
inst/extdata/demo_anno.csv
inst/extdata/human_hsk.csv
inst/extdata/metadata.csv
inst/extdata/pca_infos.csv
inst/extdata/quant/a/abundance.tsv
inst/extdata/quant/b/abundance.tsv
inst/extdata/quant/c/abundance.tsv
inst/extdata/quant/d/abundance.tsv
inst/extdata/quant/e/abundance.tsv
inst/extdata/quant/f/abundance.tsv
inst/extdata/quant/g/abundance.tsv
inst/extdata/quant/h/abundance.tsv
inst/extdata/quant_test_valid/a/abundance.tsv
inst/extdata/quant_test_valid/b/abundance.tsv
inst/extdata/quant_test_valid/c/abundance.tsv
inst/extdata/quant_test_valid/d/abundance.tsv
inst/extdata/valid_anno_multiple_transcript_type_expected_order.csv
inst/extdata/valid_anno_multiple_transcript_type_unexpected_order.csv
man/ERCC92.Rd
man/batch_de.Rd
man/batch_pca.Rd
man/batch_volcano.Rd
man/create_dummy_txi.Rd
man/deseq2_analysis.Rd
man/filter_txi.Rd
man/format_counts.Rd
man/format_de_odysse.Rd
man/format_de_results.Rd
man/get_anno_df.Rd
man/get_demo_abundance_files.Rd
man/get_demo_anno_file.Rd
man/get_demo_de_infos_file.Rd
man/get_demo_design.Rd
man/get_demo_kallisto_dir.Rd
man/get_demo_metadata_file.Rd
man/get_demo_pca_infos_file.Rd
man/get_demo_txi.Rd
man/get_demo_volcano_infos_file.Rd
man/get_filenames.Rd
man/get_human_hsk.Rd
man/get_raw_count_anno_df.Rd
man/get_ruvg_anno_df.Rd
man/get_tpm_anno_df.Rd
man/import_kallisto.Rd
man/parse_metadata_for_LO_report.Rd
man/plot_pca.Rd
man/produce_RUVSeq_graphs.Rd
man/produce_deliverables.Rd
man/produce_odysse_format.Rd
man/produce_pca.Rd
man/produce_pca_df.Rd
man/produce_report.Rd
man/produce_volcano.Rd
man/ruvg_normalization.Rd
man/split_de_results.Rd
man/validate_txi.Rd
man/wrapper_report_LO.Rd
rnaseq.Rproj
tests/testthat.R
tests/testthat/test_batch_pca.R
tests/testthat/test_dummy_txi.R
tests/testthat/test_filter_txi.R
tests/testthat/test_format.R
tests/testthat/test_get_filenames.R
tests/testthat/test_import_kallisto.R
tests/testthat/test_validate_txi.R
