--- title: BioInformatics Tools kit keywords: fastai sidebar: home_sidebar summary: "Summarized some useful tools in it." description: "Summarized some useful tools in it." nb_path: "index.ipynb" ---
BITK will help us manipulate data in different formats.
pip install bitk
usage: dedim.py [-h] [--sep SEP] [--dedimensions-method DEDIMENSIONS_METHOD]
[--cluster-method CLUSTER_METHOD]
[--assess-method ASSESS_METHOD] [--dimensions DIMENSIONS]
[--cluster-number CLUSTER_NUMBER] [-r] [--no-row-feature]
[--annotation ANNOTATION] [--size SIZE] [--style STYLE]
[-t TITLE] [-f FIG] [--version]
matrix prefix
positional arguments:
matrix matrix table, if row represents feature, please note to add '--row-feature' option
prefix output prefix
optional arguments:
-h, --help show this help message and exit
--sep SEP separation
(default: )
--dedimensions-method DEDIMENSIONS_METHOD
de-dimensions method
(default: PCA)
--cluster-method CLUSTER_METHOD
cluster method
(default: MiniBatchKMeans)
--assess-method ASSESS_METHOD
assess methods for best cluster number
(default: silhouette_score)
--dimensions DIMENSIONS
reduce to n dimensions
(default: 3)
--cluster-number CLUSTER_NUMBER
cluster number, if not specific it, it will be the best cluster number infered
(default: None)
-r, --row-feature row in the matrix represents feature
(default: True)
--no-row-feature
--annotation ANNOTATION
annotation file, sep should be ','
(default: None)
--size SIZE size column in annotation file
(default: None)
--style STYLE style column in annotation file
(default: None)
-t TITLE, --title TITLE
figure title
(default: None)
-f FIG, --fig FIG png/pdf
(default: png)
--version show program's version number and exit
usage: fc_rename.py [-h] [-s SAMPLE_TITLE] [-b BAM_TITLE] [-c COUNT_TITLE]
[--version]
featurecounts clinical prefix
featurecounts will use the bamfile name as the sample name. This script rename the featurecounts by the given table.
positional arguments:
featurecounts featurecounts table file
clinical clinical table file with header
prefix output prefix, there will be two outputs, one is count output (prefix_count.txt), and the other one is the rename featurecounts (prefix_fc.txt)
optional arguments:
-h, --help show this help message and exit
-s SAMPLE_TITLE, --sample-title SAMPLE_TITLE
the column name of the sample name
(default: sample)
-b BAM_TITLE, --bam-title BAM_TITLE
the column name of the bamfile name
(default: bam)
-c COUNT_TITLE, --count-title COUNT_TITLE
the column name used as identity in count data
(default: Geneid)
--version show program's version number and exit