Zhenjia Wang, Mete Civelek, Clint Miller, Nathan Sheffield, Michael J. If you use BART in your data analysis, please cite:īART: a transcription factor prediction tool with query gene sets or epigenomic profiles
Bart trackmap update#
Please sign up to BART users Google Group for update announcements and discussions. Is a rank of all TRs with multiple quantification scores.Īn example of BART2 output can be found here. Provides the association score of each of the TR ChIP-seq dataset with the genome cis-regulatory profile. The higher the score, the more likely the regulatory element regulates the input gene set. Is the predicted cis-regulatory profile of the input gene set and is a ranked list of all CREs (UDHS) in the genome. This is the output only generated in geneset mode. Provides regression information tells which representative H3K27ac samples are selected along with coefficients through adaptive lasso regression and sample annotations including cell line, cell type or tissue type.
In either hg38 or mm10), predict TRs enriched in this genomic region set.īart2 region -i ChIPpeak.bed -c 4 -s hg38 -outdir bart2_output Given a scored genomic region set ( BED format Given a ChIP-seq data file (mapped reads inįormat in either hg38 or mm10), predict TRs whose binding pattern associates with the input ChIP-seq profile.īart2 profile -i ChIP.bam -f bam -s hg38 -outdir bart2_output Given a query gene set in official gene symbols (HGNC for human or MGI for mouse) in text format (each gene in a row, at least 100 genes recommended), predict functional TRs that regulate these genes.īart2 geneset -i genelist.txt -s hg38 -outdir bart2_output You’ll need to modify the environment variables and add those lines in your bash file (varies on each platform, usually is ~/.bashrc or ~/.bash_profile). In this value, X.Y stands for the major–minor version of Python you are using (such as 3.5 you can find this with sys.version from a Python command line).
Bart trackmap install#
$ python setup.py install -prefix /path/to/bart $ export PYTHONPATH=/path/to/bart2/lib/pythonX.Y/site-packages/:$PYTHONPATH $ mkdir -p /path/to/bart2/lib/pythonX.Y/site-packages If you want to install everything under a specific directory, for example, a directory as /path/to/bart2/, use the following commands. By default, the script will install python library and executable codes globally. Install with root/administrator permission, or you have the
Bart trackmap download#
Modify the configure file (bart2/nf).įor example, if you download the hg38_ (and/or mm10_) and unpack it under /path/to/data, then you can modify the nf file as: To install a source distribution of BART, unpack the distribution tarball and go to the directory where you unpacked BART. Please download from the link provided above or use the following command lines. The unpacked libraries occupy 14GB hard drive storage in the download directory. You have to download the Human or Mouse Data Library under your own directory before install BART. Which include all the required python packages.ĭownload the source package and setup the configuration file Before installing BART, please make sure Python3 and the following python packages are installed. (They are NOT required for BART installation.)īART uses Python's distutils tools for source installation. The union DNaseI hypersensitive sites (UDHS) used in the BART model. The human genome hg38 and the mouse genome mm10 are supported.
Bart trackmap code#
(collected in Cistrome Data Browser) to make the prediction.īART is implemented in Python and distributed as an open-source package along with necessary data libraries.īART package is also available on Github.īART is developed and maintained by the Chongzhi Zang Lab at the University of Virginia.Ĭurrent version: 2.0, updated May 15, 2020īART2.0 for Python3 – Source code only (need to download data library separately) That bind at cis-regulatory regions to regulate gene expression in human or mouse, taking a query gene set, a ChIP-seq dataset or a scored genomic region set as input.īART leverages 7,968 human TR binding profiles and 5,851 mouse TR binding profiles from the public domain BART Binding Analysis for Regulation of TranscriptionīART ( Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcriptional regulators (TRs)
0 kommentar(er)
