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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

r-bioc-tfbstools 1.20.0+dfsg-1

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One-liner (summary)

GNU R Transcription Factor Binding Site (TFBS) Analysis

Description

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

License

Unknown

Size

874.9 KB

Downloads

Status	Completed
Checksum (MD5)	e54c70e71cf852ec8fa9a38ad1226782
Checksum (SHA-1)	4d0159dc51d5cad59d92d4ce5ee71407af2b1a6d
Checksum (SHA-256)	f0634ca01a003af6f2cc3612f1e3e6aaf41c9f5830f65076f43d756cdd3c86fd
Checksum (SHA-512)	16329ab27dd185abbf19aa1684f4aa0d49ed61facefb349442ff978128f89547de…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	8 months ago
Uploaded By
Slug Id	r-bioc-tfbstools_1200dfsg-1_armhfdeb-5otj
Unique Id	7K9TH6ClHAZg
Version (Raw)	1.20.0+dfsg-1
Version (Parsed)	Major: 1 Minor: 20 Patch: 0 Type: SemVer (Strict) Metadata: dfsg-1
	extended metadata
Homepage	https://bioconductor.org/packages/TFBSTools/
Installed Size	1.7 MB
Maintainer	Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Priority	optional
Section	gnu-r

Dependencies

Checksum (md5)

894790291b447f9241b6f9ca252a6a26

Depends	libc6	>=2.4
Depends	r-api-3.5
Depends	r-base-core	>=3.5.1-1
Depends	r-bioc-biobase	>=2.28
Depends	r-bioc-biocgenerics	>=0.14.0
Depends	r-bioc-biocparallel	>=1.2.21
Depends	r-bioc-biostrings	>=2.36.4
Depends	r-bioc-bsgenome	>=1.36.3
Depends	r-bioc-cner	>=1.4.0
Depends	r-bioc-dirichletmultinomial	>=1.10.0
Depends	r-bioc-genomeinfodb	>=1.6.1
Depends	r-bioc-genomicranges	>=1.20.6
Depends	r-bioc-iranges	>=2.2.7
Depends	r-bioc-rtracklayer	>=1.28.10
Depends	r-bioc-s4vectors	>=0.9.25
Depends	r-bioc-seqlogo	>=1.34.0
Depends	r-bioc-xvector	>=0.8.0
Depends	r-cran-catools	>=1.17.1
Depends	r-cran-dbi	>=0.6
Depends	r-cran-gtools	>=3.5.0
Depends	r-cran-rsqlite	>=1.0.0
Depends	r-cran-tfmpvalue	>=0.0.5
Depends	r-cran-xml	>=3.98-1.3
Suggests	r-cran-knitr	>=1.11
Suggests	r-cran-testthat

You can embed a badge in another website that shows this or the latest version of this package.

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[![This version of 'r-bioc-tfbstools' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'r-bioc-tfbstools' @ Cloudsmith|
.. |This version of 'r-bioc-tfbstools' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'r-bioc-tfbstools' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/1.20.0+dfsg-1/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'r-bioc-tfbstools' @ Cloudsmith" /></a>

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[![Latest version of 'r-bioc-tfbstools' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'r-bioc-tfbstools' @ Cloudsmith|
.. |Latest version of 'r-bioc-tfbstools' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'r-bioc-tfbstools' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/r-bioc-tfbstools/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'r-bioc-tfbstools' @ Cloudsmith" /></a>

rendered as:

These instructions assume you have setup the repository first (or read it).

To install/use r-bioc-tfbstools @ version 1.20.0+dfsg-1 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install r-bioc-tfbstools=1.20.0+dfsg-1

Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

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