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 Open-Source ultimaker 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).

Debian logo pscan-tfbs  1.2.2-3

One-liner (summary)

search for transcription factor binding sites

Description

Pscan finds Over-represented Transcription Factor Binding Site Motifs in Sequences from Co-Regulated or Co-Expressed Genes.

Pscan is a software tool that scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are significantly over- or under-represented, providing thus hints on which transcription factors could be common regulators of the genes studied, together with the location of their candidate binding sites in the sequences. Pscan does not resort to comparisons with orthologous sequences and experimental results show that it compares favorably to other tools for the same task in terms of false positive predictions and computation time. The website is free and open to all users and there is no login requirement.

License

Unknown

Size

59.2 KB

Downloads

0

Status  Completed
Checksum (MD5) 7c38cf9a6d4542efc705a66ed4aa096b
Checksum (SHA-1) 9d8d02b7346a7b986b7ed492315fb2cee53716e2
Checksum (SHA-256) f00415cbaf69fea07fd5fb43420b388e3e68288ad16ab19e2eee7dae267922c8
Checksum (SHA-512) 89fb4535bea35d09816979512909f0e43ff8411ac4fc5c0da047639c5dde28c906…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 6 months, 3 weeks ago
Uploaded By alex-borro
Slug Id pscan-tfbs_122-3_armhfdeb-bgch
Unique Id TLGpEe9pUeiC
Version (Raw) 1.2.2-3
Version (Parsed)
  • Major: 1
  • Minor: 2
  • Patch: 2
  • Pre (Str): (empty)
  • Pre (Num Array): 3
  • Type: SemVer (Strict)
  extended metadata
Homepage http://www.beaconlab.it/pscan
Installed Size 121.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg pscan-tfbs_1.2.2-3_armhf.deb 0
59.2 KB
md5 sha1 sha256 sha512
Package Contents (pscan-tfbs_1.2.2-3_armhf.deb)
Loading...

This package has 25 files/directories.

Dependencies

5

Checksum (md5)

2e309c8ca3cd9ff976b92690b6aca00e

Depends
libc6 >=2.4
Depends
libgcc1 >=1:3.5
Depends
libgsl23 >=2.5
Depends
libgslcblas0 >=2.4
Depends
libstdc++6 >=5.2
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|This version of 'pscan-tfbs' @ Cloudsmith|
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image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/1.2.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pscan-tfbs/1.2.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'pscan-tfbs' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pscan-tfbs/1.2.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/1.2.2-3/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'pscan-tfbs' @ Cloudsmith" /></a>

rendered as: This version of 'pscan-tfbs' @ Cloudsmith

To embed the badge for the latest package version, use the following:

[![Latest version of 'pscan-tfbs' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/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/pscan-tfbs/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)
|Latest version of 'pscan-tfbs' @ Cloudsmith|
.. |Latest version of 'pscan-tfbs' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/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/pscan-tfbs/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/
image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/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/pscan-tfbs/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'pscan-tfbs' @ Cloudsmith"]
<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pscan-tfbs/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pscan-tfbs/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'pscan-tfbs' @ Cloudsmith" /></a>

rendered as: Latest version of 'pscan-tfbs' @ Cloudsmith

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

To install/use pscan-tfbs @ version 1.2.2-3 ...

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 pscan-tfbs=1.2.2-3
Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.
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