Author: tille
Date: 2014-10-22 21:44:08 +0000 (Wed, 22 Oct 2014)
New Revision: 18375
Modified:
trunk/packages/R/r-bioc-000-dependency-scheme/3.0/BioC_3.0-dependency-tree.ditaa
Log:
Restructured dependency graph to reflect BioConductor 3.0 relations
Modified: trunk/packages/R/r-bioc-000-dependency-scheme/3.0/BioC_3.0-dependency-tree.ditaa
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.0/BioC_3.0-dependency-tree.ditaa 2014-10-22 21:43:07 UTC (rev 18374)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.0/BioC_3.0-dependency-tree.ditaa 2014-10-22 21:44:08 UTC (rev 18375)
@@ -1,85 +1,93 @@
- +------------+
- | cummerbund |
- +------------+
- ^ ^
- | |
- +--------+ +-----------+
- | |
- +---+---+ +-----+-------+ +-----------+
- | gviz | | rtracklayer | | shortread |
- +-------+ +-------------+ +---+-------+
- ^ ^ ^ :
- | | | v
- +-----+------+ +-+------+--+
- +--------------+ | biovizbase |<------------------| bsgenome |
- | altcdfenvs | +------------+ +-----------+
- +--------------+ ^ ^
- ^ ^ ^ | |
- | | | +---+---------------+ +----------+--------+
- +----------------------------------+ | | | variantannotation | | genomicalignments |
- | | | +-------------------+ +----------+--------+
- | +-----------++ | ^ ^ ^ ^ ^
- | | makecdfenv | | | : | | |
- | +------------+ | +---------+-------+ : +--+------+-+ |
- | ^ | +------------------------------------->| genomicfeatures | : | rsamtools | |
- | | | | +-----------------+ : +-----------+ |
- | | | | ^ ^ : ^ ^ |
- | | | | | | : | | |
- | | +-------------------------+ | +-----------------------------------------------------------+ | |
- | +------+---+ | | | | | : | |
-+------+-----+ | affy | +--+--+--+---+ +--------------+ +---------+ | | : | |
-| hypergraph | +----------+ | biostrings | |cAAA annotate | | biomart +-----+ | : | |
-+------------+ ^ ^ ^ ^ +------------+ +--------------+ +---------+ | : | |
- ^ | | | | ^ ^ ^ | : | |
- | +-----------+ | | +-----------------+ | | | | +--------------+ |
- | | | | | | | | | | : |
- +---+---+ +------+---------+ | | | | +------+--------+ | +----------+--+-+ : |
- | graph | | preprocesscore | | | | | | annotationdbi |----+ | genomicranges | : |
- +-------+ +----------------+ | | | | +---------------+ +---------------+ : |
- ^ | | | | ^ ^ ^ ^ : |
- | | | | | | | | | : |
- | | | | +------------------|-------------+ | | | : |
- | +-------------+ | | | | | | | : |
- | | | | | | +----------------------|---------------+ + : |
- | | | | | | | | +---------+ : |
- | | | | | | | | | : |
- | | | | | +---+---+-+ +-+-----------++ : |
- | | | | | | xvector | | genomeinfodb | : |
- | | | | | +---------+ +--------------+ : |
- | | | | | ^ ^ : |
- | | | | | | | : |
- | +------+--------+ +---+-----+ +----+--+-+ +---+-----+ | : |
- | | biocinstaller | | affyio | | biobase | | iranges +-------------------------+ : |
- | +---------------+ +---------+ +---------+ +---------+ : |
- | ^ ^ : |
- | | | : |
- +---------------------------------------------+ | | : |
- | | | : |
- | | +--+--------+ +--------------+ : |
- | | +----------------->| s4vectors | | biocparallel +--------------------------------+
- | | | +-----------+ +--------------+ :
- | | | ^ :
- | | | | :
- | | | +-------------------------------------------------------+ :
- | | | | :
- +--+--+--+---+-+ +----+-----+
+ +------------+
+ | cummerbund |
+ +------------+
+ ^
+ |
+ +---+--+
+ | gviz |
+ +------+
+ ^
+ +-------+ |
+ | edger | +------+-----+
+ +-------+ | biovizbase |
+ ^ +------+-----+
+ | ^
+ +---+---+ +------------+ +--------+ |
+ | limma | | hilbertvis | | qvalue | +----------+--------+
+ +-------+ +------------+ +--------+ | variantannotation |
+ ^ +-------------------+
+ : ^ ^
+ : | |
+ +------+------+ +------------+----+ +-+---------+
+ |cAAA go.db | | genomicfeatures | | bsgenome |
+ +-------------+ +--------------+ +-----------------+ +-----------+
+ | altcdfenvs | ^ ^ ^
+ +--------------+ | | |
+ ^ ^ ^ | +--+-------+--+
+ | | | | | rtracklayer |
+ +----------------------------------+ | | | +-------------+
+ | | | | ^
+ | +-----------++ | +-------------+ |
+ | | makecdfenv | | +-----------+ | +----------+--------+
+ | +------------+ | +-------------------------------->| shortread |<-------|---------------+ genomicalignments |
+ | ^ | | +-----------+ | +-------------------+
+ | | | | | ^ ^
+ | | | | | | |
+ | | | | | +---------+-+ |
+ | | +-------------------------+ +------------------------------------->| rsamtools | |
+ | | | | | +-----------+ |
++------+-----+ +------+---+ | +--+-----+---+ +--------------+ +----+----+ | |
+| hypergraph | | affy |<-----------+ | | biostrings | |cAAA annotate | | biomart | | |
++------------+ +----------+ | | +------------+ +--------------+ +---------+ | |
+ ^ ^ ^ ^ | | ^ ^ ^ | |
+ | | | | | | | | | | |
+ +---+---+ +----------------+ | ++--------+ | | | +------+--------+ | +----------+----+ |
+ | graph | | preprocesscore | | | affyio | | | | | annotationdbi |----+ | genomicranges | |
+ +-------+ +----------------+ | +---------+ | | | +---------------+ +---------------+ |
+ ^ | | | | ^ ^ ^ ^ |
+ | | | | | | | | | |
+ | | | | +------------------|-------------+ | | | |
+ | | | | | | | | | |
+ | | | | | | +----------------------|---------------+ + |
+ | | | | | | | | +---------+ |
+ | | | | | | | | | |
+ | | | | | +---+---+-+ +-+-----------++ |
+ | | | | | | xvector | | genomeinfodb | |
+ | | | | | +---------+ +--------------+ |
+ | | | | | ^ ^ |
+ | | | | | | | |
+ | +---------------+ +-+--+--+-+ +---+-----+ | |
+ | | biocinstaller | | biobase | | iranges +-------------------------+ |
+ | +---------------+ +---------+ +---------+ |
+ | ^ ^ |
+ | | | |
+ +---------------------------------------------+ | | |
+ | | | |
+ | | +--+--------+ +--------------+ |
+ | | +----------------->| s4vectors | | biocparallel +-----------------+
+ | | | +-----------+ +--------------+
+ | | | ^
+ | | | |
+ | | | +-------------------------------------------------------+
+ | | | |
+ +--+--+--+---+-+ +----------+
| biocgenerics +------------------------------------------------------------------>| snpstats |
+--------------+ +----------+
- +-------+
- | edger |
- +-------+
- ^
- |
-+------------+ +--------+ +---+---+
-| hilbertvis | | qvalue | | limma |
-+------------+ +--------+ +-------+
- ^
- :
- :
- +------+------+
- |cAAA go.db |
- +-------------+
+
+
+
+
+
+
+
+
+
+
+
+
+
+