Files in hugheylab/seeker
Simplified Fetching and Processing of Microarray and RNA-Seq Data
.Rbuildignore
.github/.gitignore
.github/workflows/check-deploy.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
CRAN-SUBMISSION
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/array.R
R/array_utils.R
R/fetch.R
R/install_sys_deps.R
R/qc.R
R/salmon.R
R/seeker.R
R/tximport.R
R/utils.R
README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/PRJEB38463.yml
inst/extdata/GSE25585.yml
inst/extdata/PRJNA454445.yml
inst/extdata/PRJNA600892.yml
inst/extdata/PRJNA667743.yml
inst/extdata/conda_env.yml
inst/extdata/mamba_env.yml
inst/extdata/params_template.yml
inst/extdata/platform_cdf.csv
inst/extdata/platform_mapping.csv
inst/extdata/run_seeker.R
inst/extdata/run_seeker.sh
inst/extdata/run_seeker_array.R
inst/extdata/run_seeker_array.sh
inst/extdata/user-settings.mkfg
lint_ignore.csv
man/checkDefaultCommands.Rd
man/fastqc.Rd
man/fastqscreen.Rd
man/fetch.Rd
man/fetchMetadata.Rd
man/getPlatforms.Rd
man/getSalmonMetadata.Rd
man/getTx2gene.Rd
man/installCustomCdfPackages.Rd
man/installSysDeps.Rd
man/multiqc.Rd
man/salmon.Rd
man/seeker.Rd
man/seekerArray.Rd
man/trimgalore.Rd
man/tximport.Rd
seeker.Rproj
tests/testthat.R
tests/testthat/data/E-MEXP-3696_eset.qs
tests/testthat/data/E-MEXP-3696_files.qs
tests/testthat/data/E-MTAB-8714_eset.qs
tests/testthat/data/E-MTAB-8714_files.qs
tests/testthat/data/GPL6887.qs
tests/testthat/data/GPL7202.qs
tests/testthat/data/GSE143524.yml
tests/testthat/data/GSE143524/fetch_output/SRR10876945_1.fastq.gz
tests/testthat/data/GSE143524/fetch_output/SRR10876945_2.fastq.gz
tests/testthat/data/GSE143524/fetch_output/SRR10876946_1.fastq.gz
tests/testthat/data/GSE143524/fetch_output/SRR10876946_2.fastq.gz
tests/testthat/data/GSE143524/tx2gene.csv.gz
tests/testthat/data/GSE143524_skip_all.yml
tests/testthat/data/GSE147674_eset.qs
tests/testthat/data/GSE147674_files.qs
tests/testthat/data/GSE159135.yml
tests/testthat/data/GSE167458_eset.qs
tests/testthat/data/GSE167458_files.qs
tests/testthat/data/GSE25585.yml
tests/testthat/data/GSE50143_eset.qs
tests/testthat/data/GSE50143_files.qs
tests/testthat/data/GSM5694054.yml
tests/testthat/data/LOCAL01.yml
tests/testthat/data/LOCAL01/raw/GSM311246.CEL.gz
tests/testthat/data/LOCAL01/sample_metadata.csv
tests/testthat/data/fastqc_output.qs
tests/testthat/data/fetch_metadata_output.qs
tests/testthat/data/fetch_metadata_output_2.qs
tests/testthat/data/fetch_output.qs
tests/testthat/data/get_tx2gene_output.qs
tests/testthat/data/map_pkg_ver.qs
tests/testthat/data/metadata.qs
tests/testthat/data/multiqc_output.qs
tests/testthat/data/salmon_meta_info.qs
tests/testthat/data/salmon_output.qs
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/ambig_info.tsv.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/exp3_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/exp5_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/exp_gc.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/expected_bias.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/fld.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/meta_info.json
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/obs3_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/obs5_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/obs_gc.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/observed_bias.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/aux_info/observed_bias_3p.gz
tests/testthat/data/salmon_output_exp/SAMN13836348/cmd_info.json
tests/testthat/data/salmon_output_exp/SAMN13836348/libParams/flenDist.txt
tests/testthat/data/salmon_output_exp/SAMN13836348/lib_format_counts.json
tests/testthat/data/salmon_output_exp/SAMN13836348/logs/salmon_quant.log
tests/testthat/data/salmon_output_exp/SAMN13836348/quant.sf.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/ambig_info.tsv.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/exp3_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/exp5_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/exp_gc.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/expected_bias.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/fld.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/meta_info.json
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/obs3_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/obs5_seq.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/obs_gc.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/observed_bias.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/aux_info/observed_bias_3p.gz
tests/testthat/data/salmon_output_exp/SAMN13836349/cmd_info.json
tests/testthat/data/salmon_output_exp/SAMN13836349/libParams/flenDist.txt
tests/testthat/data/salmon_output_exp/SAMN13836349/lib_format_counts.json
tests/testthat/data/salmon_output_exp/SAMN13836349/logs/salmon_quant.log
tests/testthat/data/salmon_output_exp/SAMN13836349/quant.sf.gz
tests/testthat/data/salmon_output_exp/progress.tsv
tests/testthat/data/seeker_array_ae_output.qs
tests/testthat/data/seeker_array_args_output.qs
tests/testthat/data/seeker_array_gse_output.qs
tests/testthat/data/seeker_array_local_output.qs
tests/testthat/data/seeker_output_full.qs
tests/testthat/data/seeker_output_skip.qs
tests/testthat/data/trimgalore_output.qs
tests/testthat/data/tx2gene_output.qs
tests/testthat/data/tximport_output.qs
tests/testthat/setup.R
tests/testthat/test-array-utils.R
tests/testthat/test-array.R
tests/testthat/test-fetch.R
tests/testthat/test-qc.R
tests/testthat/test-salmon.R
tests/testthat/test-seeker.R
tests/testthat/test-tximport.R
vignettes/.gitignore
vignettes/introduction.Rmd
vignettes/reproducibility.Rmd
