Index

Symbols

--add mkprobes-suggest-targets command line option --all mkprobes-transcripts command line option --allow mkprobes-candidates command line option --allow-file mkprobes-run-panel command line option --annotation mkprobes-create-dataset command line option --annotation-table mkprobes-ingest command line option --appris mkprobes-transcripts command line option --bcidx mkprobes-draw-spec command line option mkprobes-init command line option mkprobes-validate-pool command line option --blocklist-biotypes mkprobes-ingest command line option --blocklist-fasta mkprobes-create-dataset command line option --canonical mkprobes-transcripts command line option --codebook mkprobes-construct command line option mkprobes-validate-pool command line option --dataset mkprobes-init command line option --debug mkprobes command line option --delete mkprobes-assemble-MANIFEST-short command line option --disallow mkprobes-candidates command line option --dpi mkprobes-draw-spec command line option --ensembl mkprobes-transcripts command line option --existing-codebook mkprobes-make-codebook command line option --expression mkprobes-make-codebook command line option --expression-column mkprobes-make-codebook command line option --extract mkprobes-ingest command line option --fasta mkprobes-candidates command line option mkprobes-create-dataset command line option --fasta-key-regex mkprobes-create-dataset command line option mkprobes-ingest command line option --force mkprobes-init command line option --fpkm-path mkprobes-screen command line option --fpkm_path mkprobes-screen command line option --gencode mkprobes-transcripts command line option --gene mkprobes-candidates command line option mkprobes-construct command line option mkprobes-transcripts command line option --gene-name-column mkprobes-create-dataset command line option mkprobes-ingest command line option --genefile mkprobes-transcripts command line option --genes mkprobes-filter-genes command line option --genome mkprobes-ingest command line option --gtf mkprobes-create-dataset command line option mkprobes-ingest command line option --have mkprobes-suggest-targets command line option --headerfooter mkprobes-assemble command line option --ignore-revcomp mkprobes-candidates command line option --iterations mkprobes-make-codebook command line option --keep-genome mkprobes-ingest command line option --layer mkprobes-suggest-targets command line option --limit mkprobes-validate-pool command line option --list-failed mkprobes-run-panel command line option --list-failed-all mkprobes-run-panel command line option --longest mkprobes-transcripts command line option --maxoverlap mkprobes-run-panel command line option mkprobes-screen command line option --min-probes mkprobes-filter-genes command line option --minimum mkprobes-run-panel command line option mkprobes-screen command line option --mode mkprobes-convert-to-transcripts command line option

--n-bits mkprobes-make-codebook command line option --n-components mkprobes-suggest-targets command line option --no-strip-version mkprobes-create-dataset command line option mkprobes-ingest command line option --offset mkprobes-make-codebook command line option --out mkprobes-draw-spec command line option mkprobes-filter-genes command line option mkprobes-make-codebook command line option mkprobes-suggest-targets command line option --output mkprobes-candidates command line option mkprobes-run-panel command line option --overlap mkprobes-screen command line option --overwrite mkprobes-candidates command line option mkprobes-create-dataset command line option mkprobes-ingest command line option mkprobes-run-panel command line option mkprobes-screen command line option --pseudogene-limit mkprobes-candidates command line option --restriction mkprobes-construct command line option mkprobes-run-panel command line option mkprobes-screen command line option --rm-species mkprobes-assemble-MANIFEST-gen command line option --rrna-fasta mkprobes-ingest command line option --score-pcs mkprobes-suggest-targets command line option --seed mkprobes-make-codebook command line option mkprobes-suggest-targets command line option --skip-repeatmasker mkprobes-assemble-MANIFEST-gen command line option --spec mkprobes-draw-spec command line option mkprobes-validate-pool command line option --species mkprobes-create-dataset command line option mkprobes-ingest command line option mkprobes-init command line option mkprobes-prepare command line option --strip-version mkprobes-create-dataset command line option mkprobes-ingest command line option --target-probes mkprobes-construct command line option mkprobes-run-panel command line option --target_probes mkprobes-construct command line option --threads mkprobes-prepare command line option --trna-fasta mkprobes-ingest command line option --validate-only mkprobes-ingest command line option --verbose mkprobes-assemble-MANIFEST-short command line option mkprobes-transcripts command line option --which mkprobes-draw-spec command line option --workers mkprobes-run-panel command line option -c mkprobes-construct command line option mkprobes-validate-pool command line option -e mkprobes-make-codebook command line option -g mkprobes-candidates command line option mkprobes-construct command line option mkprobes-filter-genes command line option -j mkprobes-run-panel command line option -l mkprobes-screen command line option -m mkprobes-convert-to-transcripts command line option -N mkprobes-construct command line option -n mkprobes-suggest-targets command line option -o mkprobes-candidates command line option mkprobes-draw-spec command line option mkprobes-filter-genes command line option mkprobes-make-codebook command line option mkprobes-run-panel command line option mkprobes-suggest-targets command line option -r mkprobes-candidates command line option -s mkprobes-create-dataset command line option mkprobes-ingest command line option mkprobes-prepare command line option -t mkprobes-prepare command line option -v mkprobes-assemble-MANIFEST-short command line option mkprobes-transcripts command line option

C

CODEBOOK mkprobes-run-panel command line option

D

DATASET_DIR mkprobes-ingest command line option

E

EXPRESSION mkprobes-suggest-targets command line option

G

GENE mkprobes-run-panel command line option mkprobes-screen command line option

GENES mkprobes-chkgenes command line option mkprobes-convert-to-transcripts command line option mkprobes-make-codebook command line option

M

MANIFEST mkprobes-assemble command line option mkprobes-check-manifest command line option mkprobes command line option --debug mkprobes-assemble command line option --headerfooter MANIFEST mkprobes-assemble-MANIFEST-gen command line option --rm-species --skip-repeatmasker mkprobes-assemble-MANIFEST-short command line option --delete --verbose -v SHORT mkprobes-candidates command line option --allow --disallow --fasta --gene --ignore-revcomp --output --overwrite --pseudogene-limit -g -o -r PATH mkprobes-check-manifest command line option MANIFEST mkprobes-chkgenes command line option GENES PATH mkprobes-construct command line option --codebook --gene --restriction --target-probes --target_probes -c -g -N OUTPUT_PATH PATH mkprobes-convert-to-transcripts command line option --mode -m GENES PATH mkprobes-create-dataset command line option --annotation --blocklist-fasta --fasta --fasta-key-regex --gene-name-column --gtf --no-strip-version --overwrite --species --strip-version -s PATH mkprobes-draw-spec command line option --bcidx --dpi --out --spec --which -o mkprobes-filter-genes command line option --genes --min-probes --out -g -o OUTPUT_PATH mkprobes-hash command line option PATH mkprobes-ingest command line option --annotation-table --blocklist-biotypes --extract --fasta-key-regex --gene-name-column --genome --gtf --keep-genome --no-strip-version --overwrite --rrna-fasta --species --strip-version --trna-fasta --validate-only -s DATASET_DIR

mkprobes-init command line option --bcidx --dataset --force --species PROJECT mkprobes-make-codebook command line option --existing-codebook --expression --expression-column --iterations --n-bits --offset --out --seed -e -o GENES PATH mkprobes-prepare command line option --species --threads -s -t PATH mkprobes-provenance command line option PATH mkprobes-run-panel command line option --allow-file --list-failed --list-failed-all --maxoverlap --minimum --output --overwrite --restriction --target-probes --workers -j -o CODEBOOK GENE PATH mkprobes-screen command line option --fpkm-path --fpkm_path --maxoverlap --minimum --overlap --overwrite --restriction -l GENE OUTPUT_PATH mkprobes-suggest-targets command line option --add --have --layer --n-components --out --score-pcs --seed -n -o EXPRESSION mkprobes-transcripts command line option --all --appris --canonical --ensembl --gencode --gene --genefile --longest --verbose -v PATH mkprobes-validate-pool command line option --bcidx --codebook --limit --spec -c POOL

O

OUTPUT_PATH mkprobes-construct command line option mkprobes-filter-genes command line option mkprobes-screen command line option

P

PATH mkprobes-candidates command line option mkprobes-chkgenes command line option mkprobes-construct command line option mkprobes-convert-to-transcripts command line option mkprobes-create-dataset command line option mkprobes-hash command line option mkprobes-make-codebook command line option mkprobes-prepare command line option mkprobes-provenance command line option mkprobes-run-panel command line option mkprobes-transcripts command line option

POOL mkprobes-validate-pool command line option PROJECT mkprobes-init command line option

S

SHORT mkprobes-assemble-MANIFEST-short command line option