SIMBA v1.1 – SIngle-cell eMBedding Along with features

SIMBA v1.1

:: DESCRIPTION

SIMBA is a method to embed cells along with their defining features such as gene expression, transcription factor binding sequences and chromatin accessibility peaks into the same latent space.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

SIMBA

:: MORE INFORMATION

Citation

Preprint: Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam Lerer & Luca Pinello.
“SIMBA: SIngle-cell eMBedding Along with features. bioRxiv, 2021.10.17.464750v1 (2021).”

ReliefSeq – Ranking Features of Genetic Sequence data using Relief-F

ReliefSeq

:: DESCRIPTION

ReliefSeq is a feature (attribute) selection and ranking algorithm written in C++ designed to handle various types of genetic features including combinations of feature data types and endpoints (phenotypes/classes).

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ReliefSeq

:: MORE INFORMATION

Citation

PLoS One. 2013 Dec 10;8(12):e81527. doi: 10.1371/journal.pone.0081527. eCollection 2013.
ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.
McKinney BA, White BC, Grill DE, Li PW, Kennedy RB, Poland GA, Oberg AL.

pviz 0.1.12 – Dynamic JavaScript & SVG library for Visualization of Protein Sequence Features

pviz 0.1.12

:: DESCRIPTION

pViz.js is a visualization library for displaying protein sequence features in a web browser

::DEVELOPER

pviz team

:: SCREENSHOTS

pViz

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 pviz

 :: MORE INFORMATION

Citation

Visualization of protein sequence features using JavaScript and SVG with pViz.js.
Mukhyala K, Masselot A.
Bioinformatics. 2014 Aug 21. pii: btu567.

FFN – Finding Features for Nucleosomes

FFN

:: DESCRIPTION

FFN is a pattern discovery and scoring algorithm to identify feature patterns that are differentially enriched in nucleosome-forming sequences and nucleosome-depletion sequences

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 FFN

:: MORE INFORMATION

Citation:

Genomics. 2014 Jul 23. pii: S0888-7543(14)00117-7. doi: 10.1016/j.ygeno.2014.07.002. [Epub ahead of print]
Computational discovery of feature patterns in nucleosomal DNA sequences.
Zheng Y, Li X, Hu H

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