bx-python statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool bx-python
info

Tool usage distribution map

This map represents all the scientific publications referring to bx-python per scientific context
info info

Associated diseases

This word cloud represents bx-python usage per disease context
info

Popular tool citations

chevron_left Libraries/frameworks Read clustering chevron_right
Want to access the full stats & trends on this tool?

Protocols

bx-python specifications

Information


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

Download


download.png
github.png
conda.png

Versioning


No version available

Maintainer


  • person_outline James Taylor

bx-python citations

 (10)
library_books

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

2017
mSystems
PMCID: 5527300
DOI: 10.1128/mSystems.00024-17

[…] y 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 from each of the genome […]

call_split

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

2017
Nucleic Acids Res
PMCID: 5737389
PMID: 28505376
DOI: 10.1093/nar/gkx416
call_split See protocol

[…] hg19/vsMm10/reciprocalBest/). 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 […]

library_books

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

2017
BMC Genomics
PMCID: 5353786
PMID: 28302063
DOI: 10.1186/s12864-017-3617-6

[…] 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 “- […]

library_books

Inter population Differences in Retrogene Loss and Expression in Humans

2015
PLoS Genet
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 ortho […]

library_books

Sequence variants from whole genome sequencing a large group of Icelanders

2015
Sci Data
PMCID: 4413226
PMID: 25977816
DOI: 10.1038/sdata.2015.11

[…] he Ensembl Compara API was used to convert the Compara EMF files storing the multiple alignments to MAF format. For polarization of indels, ancestral sequences were retrieved from the MAF files using bx-python.Ancestral states of SNPs were inferred by comparison with the FASTA sequence for the Ensembl Compara human ancestor sequence for Homo sapiens (GRCh37).When infering the ancestral state of an […]

library_books

Genome wide comparative analysis reveals human mouse regulatory landscape and evolution

2015
BMC Genomics
PMCID: 4333152
PMID: 25765714
DOI: 10.1186/s12864-015-1245-6

[…] ChIP-Seq TFos and DHSs can be downloaded from the Mouse ENCODE web portal http://mouse.encodedcc.org/data and http://www.mouseencode.org/.The mapping software can be freely downloaded as part of the bx-python software library from https://bitbucket.org/james_taylor/bx-python/wiki/Home.Ensembl EPO 12-way alignments version 65 can be downloaded from the Ensembl (December 2011) at ftp://ftp.ensembl. […]


Want to access the full list of citations?

bx-python reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review bx-python