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

vignettes/.gitignore

vignettes/bears_vignette.Rmd

vignettes/bibliography.bib

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.

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almeidasilvaf/GEAtlas
Building Expression Atlas from RNA-Seq data

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

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almeidasilvaf/GEAtlas Building Expression Atlas from RNA-Seq data

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

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almeidasilvaf/GEAtlas
Building Expression Atlas from RNA-Seq data

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