Files in almeidasilvaf/bear
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
