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bx-python specifications


Unique identifier OMICS_18239
Name bx-python
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




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  • person_outline James Taylor <>

bx-python citations


Transcriptional Variation of Diverse Enteropathogenic Escherichia coli Isolates under Virulence Inducing Conditions

PMCID: 5527300
DOI: 10.1128/mSystems.00024-17

[…] sequenced e. coli and shigella genomes by whole-genome phylogenomic analysis as previously described (, ). the genomes were aligned using mugsy (), and homologous blocks were concatenated using the bx-python toolkit (https://bitbucket.org/james_taylor/bx-python). the columns that contained one or more gaps were removed using mothur (). the resulting 1.98-mb aligned region […]


Evolutionary re wiring of p63 and the epigenomic regulatory landscape in keratinocytes and its potential implications on species specific gene expression and phenotypes

PMCID: 5737389
PMID: 28505376
DOI: 10.1093/nar/gkx416

[…] two different software programs were used to process these alignments and find homologous regions to mouse p63 targets: ucsc liftover tool and bnmapper () implemented in bx-python (more details: https://bitbucket.org/james_taylor/bx-python/wiki/bnmapper). similar analysis was also repeated in reverse, to map the 25 920 p63 bound genomic targets in human to homologous […]


Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia

PMCID: 5353786
PMID: 28302063
DOI: 10.1186/s12864-017-3617-6

[…] with the default settings., to map genomic regions (i.e., dres, sres and himrs) from the human to the mouse genome, we used the software “bnmapper” (available at https://bitbucket.org/james_taylor/bx-python/wiki/bnmapper). the pair-wise genome alignment (chain file) between the mouse and human required by bnmapper was downloaded from the ucsc genome browser. bnmapper was run with the setting […]


Compact and highly active next generation libraries for CRISPR mediated gene repression and activation

PMCID: 5094855
PMID: 27661255
DOI: 10.7554/eLife.19760.031

[…] were calculated as described previously (), averaging the signal at each base of the target site including the pam. custom python scripts with the module bxpython (v0.5.0, https://github.com/bxlab/bx-python) to extract the processed continuous signal from the following bigwig files obtained from the encode consortium: mnase-seq https://www.encodeproject.org/files/encff000vnn/ (michael snyder […]


Genome wide predictors of NF κB recruitment and transcriptional activity

PMCID: 4661973
PMID: 26617673
DOI: 10.1186/s13040-015-0071-3

[…] overlapping peaks of tfs into sites. consequently, each site contains one or more tf peaks which overlap or are directly adjacent (no gap). specifically, we use the cluster tree implementation from bx.python (https://bitbucket.org/james_taylor/bx-python/) to find the set of all “regulatory sites”., we defined several sub-types (classes) of regulatory sites. first, we identified “inaccessible […]


Inter population Differences in Retrogene Loss and Expression in Humans

PMCID: 4608704
PMID: 26474060
DOI: 10.1371/journal.pgen.1005579

[…] whole genome alignment from ensembl release 73 [], requiring a reciprocal overlap of at least 50% between retrocopy sequences from different organisms in the alignment. to be more specific, we used bx-python package to extract genome alignment blocks corresponding to retrocopies annotated in retrogenedb. bedtools [] software was then used to find sets of overlapping blocks that constituted […]

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