Analytical framework for BS-seq data comparison and visualization.
For Python API reference manual and tutorials visit: https://shitohana.github.io/BSXplorer.
Yuditskiy, K., Bezdvornykh, I., Kazantseva, A. et al. BSXplorer: analytical framework for exploratory analysis of BS-seq data. BMC Bioinformatics 25, 96 (2024). https://doi.org/10.1186/s12859-024-05722-9
pip install bsxplorer
- bsxplorer-metagene - Create Metagene report
- bsxplorer-category - Categorize regions by P_cg metric and render HTML-report
- bsxplorer-chr - Visualize chromosome methylation levels and render HTML-report
All console scripts require configuration file – tab separated file with columns:
Column NAMES should NOT be INCLUDED in real configuration file.
| Group name | Path to report | Path to annotation | Flank length | Min region length | Region type | Genome type | Report type |
|---|---|---|---|---|---|---|---|
| Mock | mock-1.CX_report.txt | annotation.gff | 2000 | 0 | gene | gff | bismark |
| Mock | mock-2.CX_report.txt | annotation.gff | 2000 | 0 | gene | gff | bismark |
| Infected | infected-1.CX_report.txt | annotation.gff | 2000 | 0 | gene | gff | bismark |
| Infected | infected-2.CX_report.txt | annotation.gff | 2000 | 0 | gene | gff | bismark |
Columns with underlined are required.
Currently only gff genome_type and only bismark report_type are supported in colsole version of BSXplorer, although you still can read various formats from Python API.
bsxplorer-metagene --help
usage: BSXplorer [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
[--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS]
config
Metagene report creation tool
positional arguments:
config Path to config file
optional arguments:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_12-02-24_10-48-20)
--dir DIR Output and working dir (default: $CWD)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t, --threads Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
-s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
Summary function to calculate density for bin with. (default: wmean)
-u UBIN, --ubin UBIN Number of windows for upstream region (default: 50)
-d DBIN, --dbin DBIN Number of windows for downstream downstream (default: 50)
-b BBIN, --bbin BBIN Number of windows for body region (default: 100)
-q QUANTILE, --quantile QUANTILE
Quantile of most varying genes to draw on clustermap (default: 0.75)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 10)
-H VRESOLUTION Vertical resolution for heat-map (default: 100)
-V HRESOLUTION Vertical resolution for heat-map (default: 100)
--separate_strands Do strands need to be processed separately (default: False)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--ticks TICKS TICKS TICKS TICKS TICKS
Names of ticks (5 labels with ; separator in " brackets) (default: None)
bsxplorer-category --help
usage: BSXplorer-Categorise [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t] [-s {wmean,mean,median,min,max,1pgeom}] [-u UBIN] [-d DBIN] [-b BBIN] [-q QUANTILE] [-C CONFIDENCE] [-S SMOOTH] [-H VRESOLUTION] [-V HRESOLUTION]
[--separate_strands] [--export {pdf,svg,none}] [--ticks TICKS TICKS TICKS TICKS TICKS] [--cytosine_p CYTOSINE_P] [--min_cov MIN_COV] [--region_p REGION_P] [--save_cat | --no-save_cat]
config
BM, UM categorisation tool
positional arguments:
config Path to config file
optional arguments:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_12-02-24_10-51-50)
--dir DIR Output and working dir (default: $CWD)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t, --threads Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: False)
-s {wmean,mean,median,min,max,1pgeom}, --sumfunc {wmean,mean,median,min,max,1pgeom}
Summary function to calculate density for bin with. (default: wmean)
-u UBIN, --ubin UBIN Number of windows for upstream region (default: 50)
-d DBIN, --dbin DBIN Number of windows for downstream downstream (default: 50)
-b BBIN, --bbin BBIN Number of windows for body region (default: 100)
-q QUANTILE, --quantile QUANTILE
Quantile of most varying genes to draw on clustermap (default: 0.75)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 10)
-H VRESOLUTION Vertical resolution for heat-map (default: 100)
-V HRESOLUTION Vertical resolution for heat-map (default: 100)
--separate_strands Do strands need to be processed separately (default: False)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--ticks TICKS TICKS TICKS TICKS TICKS
Names of ticks (5 labels with ; separator in " brackets) (default: None)
--cytosine_p CYTOSINE_P
P-value for binomial test to consider cytosine methylated (default: .05)
--min_cov MIN_COV Minimal coverage for cytosine to keep (default: 2)
--region_p REGION_P P-value for binomial test to consider region methylated (default: .05)
--save_cat, --no-save_cat
Does categories need to be saved (default: True) (default: True)
bsxplorer-chr --help
usage: BSXplorer-ChrLevels [-h] [-o NAME] [--dir DIR] [-m BLOCK_MB] [-t THREADS] [-w WINDOW] [-l MIN_LENGTH] [-C CONFIDENCE] [-S SMOOTH] [--export {pdf,svg,none}] [--separate_strands] config
Chromosome methylation levels visualisation tool
positional arguments:
config Path to config file
optional arguments:
-h, --help show this help message and exit
-o NAME, --out NAME Output filename (default: Metagene_Report_12-02-24_10-52-40)
--dir DIR Output and working dir (default: $CWD)
-m BLOCK_MB, --block_mb BLOCK_MB
Block size for reading. (Block size ≠ amount of RAM used. Reader allocates approx. Block size * 20 memory for reading.) (default: 50)
-t THREADS, --threads THREADS
Do multi-threaded or single-threaded reading. If multi-threaded option is used, number of threads is defined by `multiprocessing.cpu_count()` (default: True)
-w WINDOW, --window WINDOW
Length of windows in bp (default: 1000000)
-l MIN_LENGTH, --min_length MIN_LENGTH
Minimum length of chromosome to be analyzed (default: 1000000)
-C CONFIDENCE, --confidence CONFIDENCE
Probability for confidence bands for line-plot. 0 if disabled (default: 0.95)
-S SMOOTH, --smooth SMOOTH
Windows for SavGol function. (default: 10)
--export {pdf,svg,none}
Export format for plots (set none to disable) (default: pdf)
--separate_strands Do strands need to be processed separately (default: False)