Author: tille
Date: 2016-05-11 15:07:50 +0000 (Wed, 11 May 2016)
New Revision: 21939
Modified:
trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa
Log:
Update dependency scheme
Modified: trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa
===================================================================
--- trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa 2016-05-11 15:07:12 UTC (rev 21938)
+++ trunk/packages/R/r-bioc-000-dependency-scheme/3.3/BioC_3.3-dependency-tree.ditaa 2016-05-11 15:07:50 UTC (rev 21939)
@@ -8,51 +8,51 @@
+------+
^
+-------+ |
- | edger | +------+-----+
- +-------+ | biovizbase |
- ^ +------+-----+
- | ^
- +---+---+ +------------+ +--------+ |
- | limma | | hilbertvis | | qvalue | +----------+--------+
- +-------+ +------------+ +--------+ | variantannotation |
- ^ +-------------------+
- : ^ ^
- : | |
- +------+------+ +------------+----+ +-+---------+
- |cAAA go.db | | genomicfeatures | | bsgenome |
- +-------------+ +--------------+ +-----------------+ +-----------+
- | altcdfenvs | ^ ^ ^
- +--------------+ | | |
- ^ ^ ^ | +--+-------+--+
- | | | | | rtracklayer |
- +----------------------------------+ | | | +-------------+
- | | | | ^
- | +-----------++ | +-------------+ |
- | | makecdfenv | | +-----------+ | +----------+--------+
- | +------------+ | +----------------------->| shortread |<-------|---------------+ genomicalignments |
- | ^ | | +-----------+ | +-------------------+
- | | | | | ^ ^
- | | | | | | |
- | | | | | +-----------+--+ +--------+-------------+
- | | +----------------+ +------------------------------------>| rsamtools | | summarizedexperiment |
- | | | | | | +--------------+ +----------------------+
- | | | | | | ^ ^: ^ ^ ^
- | | | | | | | |: : | |
- | | | | | +=============|=========|=========|:======+ | |
- | | | | | : | | |: | |
-+------+-----+ +-------+--+ | +--+-----+---+ +--------+---+ +------+--+ | |: | |
-| hypergraph | | affy |<-----------+ | | biostrings | | annotate | | biomart | | |: | |
-+------------+ +----------+ | | +------------+ +------------+ +---------+ | |: | |
- ^ ^ ^ ^ | | ^ ^ ^ | |: | |
- | | | | | | | | | | |: | |
- +---+---+ +----------------+ | ++--------+ | | | +--+----------+-+ +--------+------+ |: | |
- | graph | | preprocesscore | | | affyio | | | | | annotationdbi | | genomicranges +--|:-----------+ |
- +-------+ +----------------+ | +---------+ | | | +---------------+ +---------------+ |: |
- ^ | | | | ^ ^ ^ ^ |: |
- | | | | | | | | | |: |
- | +--------+------+ | | +---------|-----------------+ | | | |: |
- | | biocinstaller | | | | | | | | |: |
- | +---------------+ | | | | +----------------------|--------+ | |: |
+ | edger | +-----------+ +------+-----+
+ +-------+ | ensembldb +-------------------------->| biovizbase |
+ ^ +-----------+ +------+-----+
+ | ^ ^
+ +---+---+ +------------+ +--------+ | |
+ | limma | | hilbertvis | | qvalue | +-------+-------+ +----------+--------+
+ +-------+ +------------+ +--------+ | annotationhub | | variantannotation |
+ ^ +---------------+ +-------------------+
+ : ^ ^ ^ ^
+ : | | | |
+ +------+------+ | | +------------+----+ +-+---------+
+ |cAAA go.db | | | | genomicfeatures | | bsgenome |
+ +-------------+ +--------------+ | | +-----------------+ +-----------+
+ | altcdfenvs | | | ^ ^ ^
+ +--------------+ | | | | |
+ ^ ^ ^ | | | +--+-------+--+
+ | | | | | | | rtracklayer |
+ +-----------------------------+ | | +-------------------------------------+ | | +-------------+
+ | | | | | | ^
+ | +-----------++ | | | +-------------+ |
+ | | makecdfenv | | | +-----------+ | | +----------+--------+
+ | +------------+ | | +-------------------->| shortread |<----------|---------------+ genomicalignments |
+ | ^ | | | +-----------+ | | +-------------------+
+ | | | | | | | ^ ^
+ | | | | | | | | |
+ | | | | | | | +-----------+--+ +--------+-------------+
+ | | +---------------------+ +------------------------------------>| rsamtools | | summarizedexperiment |
+ | | | | | | | | +--------------+ +----------------------+
+ | | | | | | | | ^ ^: ^ ^ ^
+ | | | | | | | | | |: : | |
+ | | | | | | +=====|=======|=========|=========|:======+ | |
+ | | | | | | : | | | |: | |
++------+-----+ +-------+--+ | | +--+-----+---+ +--------+---+ | +-----+---+ | |: | |
+| hypergraph | | affy |<-----------+ | | biostrings | | annotate | | | biomart | | |: | |
++------------+ +----------+ | | | +------------+ +------------+ | +---------+ | |: | |
+ ^ ^ ^ ^ | | | ^ ^ | ^ | |: | |
+ | | | | | | | | | | | | |: | |
+ +---+---+ +----------------+ | ++--------+ | | | | +--+-----+----+-+ +--------+------+ |: | |
+ | graph | | preprocesscore | | | affyio | | | | | | annotationdbi | | genomicranges +--|:-----------+ |
+ +-------+ +----------------+ | +---------+ | | | | +---------------+ +---------------+ |: |
+ ^ | | | | | ^ ^ ^ ^ |: |
+ | | | | | | | | | | |: |
+ | ++--------------+-+ | | +---------|-----------------+ | | | |: |
+ | | biocinstaller | | | | | | | | |: |
+ | +-----------------+ | | | | +----------------------|--------+ | |: |
| | | | | | | | |: |
| | | | +---+---+-+ +-+-----------++ |: |
| | | | | xvector | | genomeinfodb | |: |