Tag: classifier

GeneCT – Cancerous Status and Tissue Origin Classifier for Pan-cancer Biopies

GeneCT

:: DESCRIPTION

GeneCT is a deep learning-based classifier for predicting cancerous status and tissue origin of pan-cancer biopsies. GeneCT showed high performance on pan-cancer datasets from various sources and outperformed existing tools.

::DEVELOPER

Dr. Sun Hao’s Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Sun K, Wang J, Wang H, Sun H.
GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies.
Bioinformatics. 2018 Dec 1;34(23):4129-4130. doi: 10.1093/bioinformatics/bty524. PMID: 29947737.

SINC – Scale-invariant Deep Neural-network Classifier for Bulk and Single-Cell RNA-seq.

SINC

:: DESCRIPTION

SINC is a deep-neural-network Classifier for Bulk and Single-Cell RNA-seq.

::DEVELOPER

Jun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX/  Linux / WIndows
  • Python

SINC

:: MORE INFORMATION

Citation

Bioinformatics, 36 (6), 1779-1784 2020 Mar 1
SINC: A Scale-Invariant Deep-Neural-Network Classifier for Bulk and Single-Cell RNA-seq Data
Chuanqi Wang , Jun Li

KNN-ID – Classifier for Discriminating Thermophilic and Mesophilic Proteins

KNN-ID

:: DESCRIPTION

KNN-ID is a new simple and effective classifier for discriminating thermophilic and mesophilic proteins.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  KNN-ID

:: MORE INFORMATION

Citation

Amino Acids. 2013 Feb;44(2):573-80. doi: 10.1007/s00726-012-1374-z. Epub 2012 Aug 1.
A similarity distance of diversity measure for discriminating mesophilic and thermophilic proteins.
Zuo YC, Chen W, Fan GL, Li QZ.

iKNN – Classifier for Non-coding RNA Identification in Organelle Genome level

iKNN

:: DESCRIPTION

According to the concept of the K-nearest neighbor technique, a novel decision-making method, an improved K-nearest neighbor classifier (iKNN) which not only use the information of quantity but also similarity distance, is introduced to recognize ncRNAs from different organelle genomes.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  iKNN

:: MORE INFORMATION

Citation

Using the Chou’s pseudo component to predict the ncRNA locations based on the improved K-nearest neighbor (iKNN) classifier.
In prepared.

Genome Classifier – Genomic Signature Classifier

Genome Classifier

:: DESCRIPTION

Genome Classifier (genomeclass) is a python/pyrex implementation of the Bayesian classifier of genomic signatures.

::DEVELOPER

Sandberg Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 Genome Classifier

:: MORE INFORMATION

Citation

Genome Res. 2001 Aug;11(8):1404-9.
Capturing whole-genome characteristics in short sequences using a naïve Bayesian classifier.
Sandberg R, Winberg G, Bränden CI, Kaske A, Ernberg I, Cöster J.

CLaMS / iClaMS – Classifier for Metagenomic Sequences

CLaMS / iClaMS

:: DESCRIPTION

ClaMS is a metagenome binning/clustering tool. It bins sequences to user-defined training sets by comparing signatures computed from their composition.

iClaMS consists of a Perl wrapper script that separates a sequence set into bins by training on the sequence set itself. Directions for running both ClaMS and iClaMS are included in the README in the tar archive.

::DEVELOPER

DOE Joint Genome Institute

:: SCREENSHOTS

ClaMS

::REQUIREMENTS

  • Linux / MacOsX /Windows
  • Java

:: DOWNLOAD

 CLaMS / iClaMS

:: MORE INFORMATION

Citation

ClaMS: A Classifier for Metagenomic Sequences.
Pati A, Heath LS, Kyrpides NC, Ivanova N.
Stand Genomic Sci. 2011 Nov 30;5(2):248-53. doi: 10.4056/sigs.2075298. Epub 2011 Nov 28.

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