Index

Symbols

--annotationfile, --annotation <annotationfile> CLI-Reference-create command line option --debug, --no-debug CLI-Reference command line option --expmeta <expmeta> CLI-Reference-create command line option --force CLI-Reference-metadata-delete command line option CLI-Reference-metadata-set command line option CLI-Reference-rnaseq-delete command line option CLI-Reference-rnaseq-set command line option --format <format> CLI-Reference-dump-coverage command line option --horizontal CLI-Reference-plot-regioncounts command line option --lengthmax, --max <lengthmax> CLI-Reference-create command line option --lengthmin, --min <lengthmin> CLI-Reference-create command line option --lengthsfile, --lengths <lengthsfile> CLI-Reference-create command line option --lowerlength <lowerlength> CLI-Reference-dump-coverage command line option CLI-Reference-dump-region-counts command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option --meta <meta> CLI-Reference-metadata-set command line option --metageneradius, --radius <metageneradius> CLI-Reference-create command line option --name <name> CLI-Reference-create command line option CLI-Reference-metadata-delete command line option CLI-Reference-metadata-get command line option CLI-Reference-metadata-set command line option CLI-Reference-rnaseq-delete command line option CLI-Reference-rnaseq-get command line option --nocoverage CLI-Reference-create command line option --normalize CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option --nosumtrans CLI-Reference-dump-metagene command line option --out <out> CLI-Reference-rnaseq-get command line option --reference <reference> CLI-Reference-create command line option --ribometa <ribometa> CLI-Reference-create command line option --sep <sep> CLI-Reference-rnaseq-get command line option CLI-Reference-rnaseq-set command line option --sumlengths CLI-Reference-dump-metagene command line option CLI-Reference-dump-region-counts command line option

--sumtrans CLI-Reference-dump-region-counts command line option --upperlength <upperlength> CLI-Reference-dump-coverage command line option CLI-Reference-dump-region-counts command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option -a, --alignment <alignment> CLI-Reference-rnaseq-set command line option -a, --alignmentfile <alignmentfile> CLI-Reference-create command line option -c, --counts <counts> CLI-Reference-rnaseq-set command line option -d, --dump <dump> CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option -e, --experiment <experiment> CLI-Reference-dump-metagene command line option CLI-Reference-dump-region-counts command line option -f, --alignmentformat <alignmentformat> CLI-Reference-create command line option -f, --format <format> CLI-Reference-rnaseq-set command line option -l, --leftspan <leftspan> CLI-Reference-create command line option -l, --lowerlength <lowerlength> CLI-Reference-dump-metagene command line option -n, --name <name> CLI-Reference-rnaseq-set command line option -n, --nprocess <nprocess> CLI-Reference-create command line option -o, --out <out> CLI-Reference-dump-annotation command line option CLI-Reference-dump-coverage command line option CLI-Reference-dump-metagene command line option CLI-Reference-dump-reference-lengths command line option CLI-Reference-dump-region-counts command line option CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option -r, --region <region> CLI-Reference-dump-region-counts command line option CLI-Reference-plot-lengthdist command line option -r, --rightspan <rightspan> CLI-Reference-create command line option -s, --sep <sep> CLI-Reference-dump-reference-lengths command line option -s, --site <site> CLI-Reference-dump-metagene command line option CLI-Reference-plot-metagene command line option -t, --title <title> CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option -u, --upperlength <upperlength> CLI-Reference-dump-metagene command line option

C

CLI-Reference command line option --debug, --no-debug CLI-Reference-create command line option --annotationfile, --annotation <annotationfile> --expmeta <expmeta> --lengthmax, --max <lengthmax> --lengthmin, --min <lengthmin> --lengthsfile, --lengths <lengthsfile> --metageneradius, --radius <metageneradius> --name <name> --nocoverage --reference <reference> --ribometa <ribometa> -a, --alignmentfile <alignmentfile> -f, --alignmentformat <alignmentformat> -l, --leftspan <leftspan> -n, --nprocess <nprocess> -r, --rightspan <rightspan> RIBOFILE CLI-Reference-dump-annotation command line option -o, --out <out> RIBO CLI-Reference-dump-coverage command line option --format <format> --lowerlength <lowerlength> --upperlength <upperlength> -o, --out <out> EXPERIMENT RIBO CLI-Reference-dump-metagene command line option --nosumtrans --sumlengths -e, --experiment <experiment> -l, --lowerlength <lowerlength> -o, --out <out> -s, --site <site> -u, --upperlength <upperlength> RIBO CLI-Reference-dump-reference-lengths command line option -o, --out <out> -s, --sep <sep> RIBO CLI-Reference-dump-region-counts command line option --lowerlength <lowerlength> --sumlengths --sumtrans --upperlength <upperlength> -e, --experiment <experiment> -o, --out <out> -r, --region <region> RIBO CLI-Reference-info command line option RIBOFILE CLI-Reference-merge command line option IN_RIBO_PATHS OUT_RIBO_PATH

CLI-Reference-metadata-delete command line option --force --name <name> RIBO CLI-Reference-metadata-get command line option --name <name> RIBO CLI-Reference-metadata-set command line option --force --meta <meta> --name <name> RIBO CLI-Reference-plot-lengthdist command line option --normalize -d, --dump <dump> -o, --out <out> -r, --region <region> -t, --title <title> EXPERIMENTS RIBO CLI-Reference-plot-metagene command line option --lowerlength <lowerlength> --normalize --upperlength <upperlength> -d, --dump <dump> -o, --out <out> -s, --site <site> -t, --title <title> EXPERIMENTS RIBO CLI-Reference-plot-regioncounts command line option --horizontal --lowerlength <lowerlength> --upperlength <upperlength> -d, --dump <dump> -o, --out <out> -t, --title <title> EXPERIMENTS RIBO CLI-Reference-rnaseq-delete command line option --force --name <name> RIBO CLI-Reference-rnaseq-get command line option --name <name> --out <out> --sep <sep> RIBO CLI-Reference-rnaseq-set command line option --force --sep <sep> -a, --alignment <alignment> -c, --counts <counts> -f, --format <format> -n, --name <name> RIBO

E

EXPERIMENT CLI-Reference-dump-coverage command line option EXPERIMENTS CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option

I

IN_RIBO_PATHS CLI-Reference-merge command line option

O

OUT_RIBO_PATH CLI-Reference-merge command line option

R

RIBO CLI-Reference-dump-annotation command line option CLI-Reference-dump-coverage command line option CLI-Reference-dump-metagene command line option CLI-Reference-dump-reference-lengths command line option CLI-Reference-dump-region-counts command line option CLI-Reference-metadata-delete command line option CLI-Reference-metadata-get command line option CLI-Reference-metadata-set command line option CLI-Reference-plot-lengthdist command line option CLI-Reference-plot-metagene command line option CLI-Reference-plot-regioncounts command line option CLI-Reference-rnaseq-delete command line option CLI-Reference-rnaseq-get command line option CLI-Reference-rnaseq-set command line option

RIBOFILE CLI-Reference-create command line option CLI-Reference-info command line option