Difference between revisions of "DiChIPHorde (analysis)"
From BioUML platform
(Mistaken file names update reverted) |
(Class name added) |
||
| Line 3: | Line 3: | ||
;Provider | ;Provider | ||
:[[Autosome.Ru]] | :[[Autosome.Ru]] | ||
| + | ;Class | ||
| + | :{{Class|biouml.plugins.chipmunk.DiChipHordeAnalysis}} | ||
;Plugin | ;Plugin | ||
:[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]] | :[[Biouml.plugins.chipmunk (plugin)|biouml.plugins.chipmunk (ChIPMunk plugin)]] | ||
Revision as of 11:14, 31 May 2013
- Analysis title
DiChIPHorde
- Provider
- Autosome.Ru
- Class
DiChipHordeAnalysis- Plugin
- biouml.plugins.chipmunk (ChIPMunk plugin)
Description
The DiChIPHorde extension can be used to discover multiple significant di-nucleotide motifs in a given dataset using two independent filtering strategies.
Parameters:
- Input sequences – Collection containing input reads.
- Start length – Start length of the matrix
- Stop length – Stop length of the matrix
- Motifs count limit – Maximum number of motifs to discover
- Filtering mode – Whether to mask polyN ("Mask") or to drop entire sequence ("Filter")
- Number of threads (expert) – Number of concurrent threads when processing
- Step limit (expert) – Step limit
- Try limit (expert) – Try limit
- Local background (expert) – If checked, local background estimation is used. Otherwise uniform background estimation is used
- ZOOPS factor (expert) – Zero-or-one-occurence-per-sequence factor
- Motif shape (expert) – Motif shape
- Use peak profiles (expert) – Whether to use peak profiles (if available)
- Output matrix library – Path to the matrix library to put matrix into (will be created if not specified)
- Matrix name prefix – Prefix for the matrix name. It will be followed by number.
More about DiChIPMunk at: http://autosome.ru/dichipmunk/
