Files in almeidasilvaf/GEAtlas
Building Expression Atlas from RNA-Seq data

.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md .github/CONTRIBUTING.md .github/ISSUE_TEMPLATE/issue_template.md .github/SUPPORT.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
Dockerfile
NAMESPACE
NEWS.md R/00_get_metadata.R R/01_download_data.R R/02_qc.R R/03_read_filtering.R R/04_read_mapping.R R/05_01_quantification_salmon.R R/05_02_quantification_kallisto.R R/05_03_quantification_featureCounts.R R/05_04_assembly_quantification_stringtie.R R/check_dependencies.R R/data.R R/utils.R README.Rmd README.md
codecov.yml
data-raw/data_acquisition.md
data/mapping_qc.rda
data/sample_info.rda
data/tx2gene.rda
dev/01_create_pkg.R dev/02_git_github_setup.R dev/03_core_files.R dev/04_update.R
inst/_pkgdown.yml
inst/extdata/Homo_sapiens.GRCh37.75_subset.bed
inst/extdata/Homo_sapiens.GRCh37.75_subset.fa
inst/extdata/Homo_sapiens.GRCh37.75_subset.gtf
inst/extdata/Homo_sapiens.GRCh37.75_subset_transcripts.fa.gz
inst/extdata/SAMN02422669/abundance.tsv
inst/extdata/SAMN02422669/aux_info/ambig_info.tsv
inst/extdata/SAMN02422669/aux_info/eq_classes.txt.gz
inst/extdata/SAMN02422669/aux_info/exp3_seq.gz
inst/extdata/SAMN02422669/aux_info/exp5_seq.gz
inst/extdata/SAMN02422669/aux_info/exp_gc.gz
inst/extdata/SAMN02422669/aux_info/expected_bias.gz
inst/extdata/SAMN02422669/aux_info/fld.gz
inst/extdata/SAMN02422669/aux_info/meta_info.json
inst/extdata/SAMN02422669/aux_info/obs3_seq.gz
inst/extdata/SAMN02422669/aux_info/obs5_seq.gz
inst/extdata/SAMN02422669/aux_info/obs_gc.gz
inst/extdata/SAMN02422669/aux_info/observed_bias.gz
inst/extdata/SAMN02422669/aux_info/observed_bias_3p.gz
inst/extdata/SAMN02422669/cmd_info.json
inst/extdata/SAMN02422669/libParams/flenDist.txt
inst/extdata/SAMN02422669/lib_format_counts.json
inst/extdata/SAMN02422669/logs/salmon_quant.log
inst/extdata/SAMN02422669/quant.sf
inst/extdata/SAMN02422669Aligned.sortedByCoord.out.bam
inst/extdata/SAMN02422669Log.final.out
inst/extdata/SRR1039508.json
inst/extdata/SRR1039508_1.fastq.gz
inst/extdata/SRR1039508_2.fastq.gz
inst/extdata/bac_16s_subset.fa
inst/extdata/fastqc_env.yml
inst/extdata/kallisto_env.yml
inst/extdata/multiqc_env.yml
inst/extdata/rseqc_env.yml
inst/extdata/salmon_env.yml
inst/extdata/sortmerna_env.yml
inst/extdata/star_env.yml
inst/extdata/stringtie_env.yml
inst/extdata/subread_env.yml
inst/extdata/taco_env.yml
inst/extdata/trimmomatic_env.yml
inst/scripts/create_environment.R inst/scripts/example_workflow_with_conda.R man/check_md5.Rd man/create_dir_structure.Rd man/create_sample_info.Rd man/download_from_ena.Rd man/fastp_is_installed.Rd man/fastq_exists.Rd man/featureCounts.Rd man/featureCounts2se.Rd
man/figures/README-pressure-1.png
man/figures/logo.png
man/get_url_ena.Rd man/gff2bed.Rd man/infer_strandedness.Rd man/kallisto2se.Rd man/kallisto_index.Rd man/kallisto_is_installed.Rd man/kallisto_quantify.Rd man/mapping_pass.Rd man/mapping_qc.Rd man/multiqc_is_installed.Rd man/remove_rrna.Rd man/rseqc_is_installed.Rd man/salmon2se.Rd man/salmon_index.Rd man/salmon_is_installed.Rd man/salmon_quantify.Rd man/sample_info.Rd man/sortmerna_is_installed.Rd man/star_align.Rd man/star_genome_index.Rd man/star_is_installed.Rd man/stringtie2se.Rd man/stringtie_assemble.Rd man/stringtie_is_installed.Rd man/stringtie_quantify.Rd man/subread_is_installed.Rd man/summary_stats_fastp.Rd man/summary_stats_salmon.Rd man/summary_stats_star.Rd man/taco_is_installed.Rd man/taco_merge.Rd man/translate_strandedness.Rd man/trim_reads.Rd man/tx2gene.Rd tests/testthat.R tests/testthat/test-00_get_metadata.R tests/testthat/test-01_download_data.R tests/testthat/test-02_qc.R tests/testthat/test-03_read_filtering.R tests/testthat/test-04_read_mapping.R tests/testthat/test-05_01_quantification_salmon.R tests/testthat/test-05_02_quantification_kallisto.R tests/testthat/test-05_03_quantification_featureCounts.R tests/testthat/test-05_04_assembly_quantification_stringtie.R tests/testthat/test-check_dependencies.R tests/testthat/test-utils.R
vignettes/.gitignore
vignettes/bears_vignette.Rmd
vignettes/bibliography.bib
almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.