✅
usage: clust [-h] [-n <file or int> [<file or int> ...]] [-r <file>] [-m <file>] [-o <directory>]
[-t <real number>] [-basemethods <string> [<string> ...]]
[-K <integer> [<integer> ...]] [-s <real number>] [-d <integer>]
[-fil-v <real number>] [-fil-c <integer>] [-fil-d <integer>] [--fil-abs] [--fil-perc]
[--fil-flat] [--no-fil-flat] [-cs <integer>] [-q3s <real number>] [--no-optimisation]
[--deterministic] [-np <integer>]
datapath
/===========================================================================\
| Clust |
| Optimised consensus clustering of multiple heterogeneous datasets |
| Version v1.17.0 |
| |
| By Dr Basel Abu-Jamous |
| while at |
| Department of Plant Sciences |
| The University of Oxford |
| baselabujamous@gmail.com |
+---------------------------------------------------------------------------+
| Citation |
| ~~~~~~~~ |
| When publishing work that uses Clust, please cite: |
| Basel Abu-Jamous and Steven Kelly (2018) Clust: automatic extraction of |
| optimal co-expressed gene clusters from gene expression data. Genome |
| Biology 19:172; doi: https://doi.org/10.1186/s13059-018-1536-8. |
+---------------------------------------------------------------------------+
| Full description of usage can be found at: |
| https://github.com/BaselAbujamous/clust |
\===========================================================================/
positional arguments:
datapath Data file path or directory with data file(s).
optional arguments:
-h, --help show this help message and exit
-n <file or int> [<file or int> ...]
Normalisation file or list of codes (default: 1000)
-r <file> Replicates structure file
-m <file> OrthoGroups (OGs) mapping file
-o <directory> Output directory
-t <real number> Cluster tightness (default: 1.0).
-basemethods <string> [<string> ...]
One or more base clustering methods (default: k-means)
-K <integer> [<integer> ...]
K values, e.g. 2 4 6 10 ... (default: 4 to 20 (step=4))
-s <real number> Outlier standard deviations (default: 3.0)
-d <integer> Min datasets in which a gene must exist (default: 1)
-fil-v <real number> Filtering: gene expression threshold (default: -inf)
-fil-c <integer> Filtering: number of conditions (default: 0)
-fil-d <integer> Filtering: number of datasets (default: 0)
--fil-abs Filter using absolute values of expression
--fil-perc -fil-v is a percentile of genes rather than raw value
--fil-flat Filter out genes with flat expression profiles (default)
--no-fil-flat Cancels the default --fil-flat option
-cs <integer> Smallest cluster size (default: 11)
-q3s <real number> Q3s defining outliers (default: 2.0)
--no-optimisation Skip cluster optimsation & completion
--deterministic Obsolete. All steps are already deterministic (v1.7.4+)
-np <integer> Obsolete. Number of parallel processes (default: 1)