diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 00000000..e69de29b diff --git a/404.html b/404.html new file mode 100644 index 00000000..3ba82b26 --- /dev/null +++ b/404.html @@ -0,0 +1,466 @@ + + + +
+ + + + + + + + + + + + + + + + + + +The byconaut
repository provides a number of helper applications with different
+types of functionalities, e.g.
These applications are in some way used to populate or manage data resources for
+bycon
driven implementations of the Beacon protokol (i.e. genomic data resources).
For more information see the dedicated documentation page).
+analysesStatusmapsRefresher
¶This is one of the housekeeping scripts which has to be run after CNV data has +been added or modified in the database. It creates CNV status data for binned +genome intervals, used for histogram generation, sample clustering etc., +as well as some other statistics (e.g. CNV coverage per chromosomal arms ...).
+-d
, --datasetIds
... to select the dataset (only one per run)--filters
... to (optionally) limit the processing to a subset of samples
+ (e.g. after a limited update)bin/analysesStatusmapsRefresher.py -d progenetix
bin/analysesStatusmapsRefresher.py -d progenetix --filters "pgx:icdom-81703"
bin/analysesStatusmapsRefresher.py -d cellz --filters "cellosaurus:CVCL_0312"
collationsCreator
¶The collationsCreator
script updates the dataset specific collations
collections
+which provide the aggregated data (sample numbers, hierarchy trees etc.) for all
+individual codes belonging to one of the entities defined in the filter_definitions
+in the bycon
configuration. The (optional) hierarchy data is provided
+in rsrc/classificationTrees/__filterType__/numbered-hierarchies.tsv
as a list
+of ordered branches in the format code | label | depth | order
.
TBD The filter definition should be one of the configuration where users can
+provide additions and overrides in the byconaut/local
directory.
-d
, --datasetIds
... to select the dataset (only one per run)--filters
... to (optionally) limit the processing to a subset of samples
+ (e.g. after a limited update)bin/collationsCreator.py -d progenetix
bin/collationsCreator.py -d examplez --collationTypes "PMID"
frequencymapsCreator
¶This app creates the frequency maps for the "collations" collection. Basically, +all samples matching any of the collation codes and representing CNV analyses +are selected and the frequencies of CNVs per genomic bin are aggregated. The +result contains teh gain and loss frquencies for all genomic intervals, for the +given entity.
+-d
, --datasetIds
... to select the dataset (only one per run)--collationTypes
... to (optionally) limit the processing to a selected
+ collation types (e.g. NCIT
, PMID
, icdom
...)bin/frequencymapsCreator.py -d progenetix
bin/frequencymapsCreator.py -d examplez --collationTypes "icdot"
ISCNsegmenter
¶This is a helper app to transform cytogenetic CGH annotations (rev ish) to the
+canonical tab-delimited .pgxseg
segment file format.
bin/ISCNsegmenter.py -i imports/ccghtest.tab -o exports/cghtest-with-histo.pgxseg