Files in uashogeschoolutrecht/structural_colours
Package For Project Structural Colour
.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
NAMESPACE
R/CAT_taxonomy_to_krona_format.R
R/add_accession_contigs_megahit_dir.R
R/archive/ASCII_range_concatenated_qualities.R
R/archive/MGYS00000974.R
R/archive/add_accession_contigs_megahit.R
R/archive/append_fastq_to_fastq.R
R/archive/cog.R
R/archive/concatenate_fastq_qualities.R
R/archive/download_data.R
R/archive/download_sc.R
R/archive/get_MGYS00000974.R
R/archive/get_MGYS00000991.R
R/archive/get_MGYS00005036.R
R/archive/get_sc_data.R
R/archive/make_tmap.R
R/archive/notdone.R
R/archive/pipeline.R
R/archive/q2_metaphlan2.R
R/archive/rescale_phred_score_fastqfile.R
R/archive/run_kraken2.R
R/archive/substract_substring_fasta.R
R/archive/tblastn.R
R/archive/trimlog_stats.R
R/blast.R
R/cat_rename_seq-id.R
R/combine_pipeline_output.R
R/fastqc_multisummary.R
R/gbtools.R
R/get_data_ebi.R
R/get_fastq.R
R/get_filereport.R
R/get_metadata.R
R/grinder.R
R/ktImportText.R
R/makeblastdb.R
R/pipeline_single.R
R/quast_summary.R
R/run_CAT.R
R/run_bbmap.R
R/run_fastqc.R
R/run_megahit.R
R/run_metabat2.R
R/run_prokka.R
R/run_quast.R
R/run_trimmomatic.R
R/server.R
R/sparklyr_script.R
R/ui.R
README.md
data-raw/get_data.sh
data/MGYS00000974.rda
data/MGYS00000991.rda
data/MGYS00005036.rda
data/filereport.rda
data/filereport_PRJEB14154.rda
data/filereport_PRJEB26733.rda
data/filereport_PRJNA415974.rda
data/metadata
inst/archive/get_sc_data.sh
inst/archive/kraken_build.sh
inst/archive/megahit_arc.sh
inst/archive/megahit_compost.sh
inst/archive/metaphlan.sh
inst/archive/metaspades.sh
inst/archive/qiime.sh
inst/archive/rescaling_ERR833272.Rmd
inst/archive/trimmomatic.sh
inst/archive/workflow.Rmd
inst/docker/DockerConfig/config/rclone.conf
inst/docker/DockerConfig/mount.sh
inst/docker/DockerConfig/requirements.R
inst/docker/Dockerfile
inst/docker/build_docker.sh
inst/docker/install_docker.sh
inst/docker/run_docker.sh
inst/extdata/GCA_002277835.1_ASM227783v1_genomic.fna
inst/extdata/GCA_002277835.1_ASM227783v1_genomic.gff
inst/extdata/GCA_002277835.1_ASM227783v1_genomic.gtf
inst/extdata/GCA_002277835.1_ASM227783v1_protein.faa
inst/extdata/M17.txt
inst/extdata/MGYS00000974.csv
inst/extdata/MGYS00000991.csv
inst/extdata/MGYS00000991_clean.csv
inst/extdata/MGYS00005036.csv
inst/extdata/cogs.csv
inst/extdata/filereport_PRJEB14154
inst/extdata/filereport_PRJEB26733
inst/extdata/filereport_PRJEB4331
inst/extdata/filereport_PRJEB8968
inst/extdata/filereport_PRJNA365003
inst/extdata/filereport_PRJNA415974
inst/extdata/gldiB.txt
inst/extdata/sc_markers.faa
inst/get_data_ebi.sh
inst/images/sample_points.png
inst/ktImportText.sh
inst/megahit.sh
inst/metabat2.sh
inst/prokka.sh
logs/log4j.spark.log
logs/log4j.spark.log.2020-03-10
logs/log4j.spark.log.2020-04-08
logs/log4j.spark.log.2020-05-14
logs/log4j.spark.log.2020-05-15
logs/log4j.spark.log.2020-05-16
man/add_accession_contigs_megahit_dir.Rd
man/blast.Rd
man/cat_rename_seq_id.Rd
man/fastqc_multisummary.Rd
man/gbtools_plot.Rd
man/get_data_ebi.Rd
man/get_fastq.Rd
man/get_filereport.Rd
man/get_metadata.Rd
man/grinder.Rd
man/makeblastdb.Rd
man/run_CAT.Rd
man/run_bbmap.Rd
man/run_fastqc.Rd
man/run_megahit.Rd
man/run_metabat2.Rd
man/run_prokka.Rd
man/run_sc_pipeline.Rd
man/run_trimmomatic.Rd
scpackage.Rproj
tests/testthat.R
vignettes/.gitignore
vignettes/scpackage_vignette.Rmd
