Category: Miscellaneous

PubSearch 0.8.1 – Literature Curation Management System

PubSearch 0.8.1

:: DESCRIPTION

PubSearch is a literature curation management system designed to store and manage the available literature for an organism or system of interest. It provides database curators with a powerful literature search capability, stores relevant biological information, creates automatic associations between the biological information and the literature, and provides a user-friendly web interface for manual validation and curation.

::DEVELOPER

PubSearch Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PubSearch

:: MORE INFORMATION

Citation

Yoo, D, Xu, I, Berardini, T, Rhee, S, Narayanasamy, V, Twigger, S (2006)
PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature..
Curr Protoc Bioinformatics. 2006 Mar;Chapter 9:Unit9.7.

BLOSpectrum 20091230 – Split BLOSUM Score into numbers of Biological Significance

BLOSpectrum 20091230

:: DESCRIPTION

 BLOSpectrum is a software of splitting the BLOSUM score into numbers of biological significance.

::DEVELOPER

Bioinfor lab, Dipartimento di Matematica e Informatica, Università degli Studi di Trieste

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

  BLOSpectrum

:: MORE INFORMATION

Citation

Splitting the BLOSUM score into numbers of biological significance.
Fabris F, Sgarro A, Tossi A.
EURASIP J Bioinform Syst Biol. 2007:31450.

ACD/Column Selector – Search & Choose Columns

ACD/Column Selector

:: DESCRIPTION

ACD/Column Selector  application from ACD/Labs helps chromatographers select suitable alternatives to a desired chromatographic column, closely matched for retention and selectivity, based on the Tanaka chromatographic parameters.

::DEVELOPER

Advanced Chemistry Development

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

NO

:: MORE INFORMATION

Ref.

Euerby, MR; Petersson, P.
Chromatographic classification and comparison of commercially available reversed-phase liquid chromatographic columns using principal component analysis.
J. Chromatogr. A, 994: 13–36, 2003.

CellVGAE – Unsupervised scRNA-seq analysis Workflow with Graph Attention Networks

CellVGAE

:: DESCRIPTION

CellVGAE uses the connectivity between cells (such as k-nearest neighbour graphs or KNN) with gene expression values as node features to learn high-quality cell representations in a lower-dimensional space, with applications in downstream analyses like (density-based) clustering, visualisation, gene set enrichment analysis and others.

::DEVELOPER

CellVGAE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CellVGAE

:: MORE INFORMATION

Citation:

Buterez D, Bica I, Tariq I, Andrés-Terré H, Liò P.
CellVGAE: an unsupervised scRNA-seq analysis workflow with graph attention networks.
Bioinformatics. 2021 Dec 2:btab804. doi: 10.1093/bioinformatics/btab804. Epub ahead of print. PMID: 34864884.

Baescs 2.0 – Estimate Calibration Curves and unknown Concentrations in Immunoassays

Baescs 2.0

:: DESCRIPTION

Baescs is a Bayesian approach to estimate calibration curves and unknown concentrations in immunoassays.

::DEVELOPER

The Center for Computational Immunology 

:: SCREENSHOTS

Baescs

::REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Baescs

:: MORE INFORMATION

Citation

Feng Feng; Ana Paula Sales; Thomas B. Kepler :
A Bayesian approach for estimating calibration curves and unknown concentrations in immunoassays.
Bioinformatics (2011) 27 (5): 707-712.

sppPCA 1.0 – Sequential Projection Pursuit PCA

sppPCA 1.0

:: DESCRIPTION

The sppPCA method presented here provides an approach for researchers to perform exploratory data analysis on new -omic datasets containing missing data. By removing the necessity to impute missing values, the results of the low-dimensional projections of the data are not skewed by inaccurate estimates of variance, which is often introduced by imputation. Sequential projection pursuit (SPP) is a computationally robust approach for performing the optimization task to identify the small subset of orthogonal latent variables of interest (e.g., principal components).

:: DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

sppPCA

:: REQUIREMENTS

  • Windows
  • Matlab
  • JAVA

:: DOWNLOAD

 sppPCA

:: MORE INFORMATION

Citation

Biotechniques. 2013 Mar;54(3):165-8. doi: 10.2144/000113978.
Sequential projection pursuit principal component analysis–dealing with missing data associated with new -omics technologies.
Webb-Robertson BJ, Matzke MM, Metz TO, McDermott JE, Walker H, Rodland KD, Pounds JG, Waters KM.

Gigwa 2.4.1 – Genotype Investigator for Genome Wide Analyse

Gigwa 2.4.1

:: DESCRIPTION

The Gigwa application provides an easy and intuitive way to explore large amounts of genotyping data by filtering it not only on the basis of variant features, including functional annotations, but also matching genotype patterns. It is a fairly lightweight, web-based, platform-independent solution that may be deployed on a workstation or as a data portal. It allows to feed a MongoDB database with VCF, PLINK or HapMap files containing up to tens of billions of genotypes, and provides a user-friendly interface to filter data in real time.

:: DEVELOPER

South Green bioinformatics platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

Gigwa

:: MORE INFORMATION

Citation

Gigwa v2-Extended and improved genotype investigator.
Sempéré G, Pétel A, Rouard M, Frouin J, Hueber Y, De Bellis F, Larmande P.
Gigascience. 2019 May 1;8(5). pii: giz051. doi: 10.1093/gigascience/giz051.

Gigwa-Genotype investigator for genome-wide analyses.
Sempéré G, Philippe F, Dereeper A, Ruiz M, Sarah G, Larmande P.
Gigascience. 2016 Jun 6;5:25. doi: 10.1186/s13742-016-0131-8.

CATT 1.9 – CharActerzing TCR Repertoires

CATT 1.9

:: DESCRIPTION

CATT is a tool for detecting CDR3 sequences from any TCR containing raw sequencing data (including TCR-seq, RNA-seq, scRNA-seq and any TCR contained sequencing data).

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Julia

:: DOWNLOAD

CATT

:: MORE INFORMATION

Citation

Chen SY, Liu CJ, Zhang Q, Guo AY.
An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data.
Bioinformatics. 2020 Aug 1;36(15):4255-4262. doi: 10.1093/bioinformatics/btaa432. PMID: 32399561.

FFLtool – Web Server for TF-miRNA-target Feed Forward Loop analysis

FFLtool

:: DESCRIPTION

FFLtool is a webserver for analyzing Feed Forward Loop (FFL) regulatory motifs among transcription factors (TFs), microRNAs (miRNAs) and genes.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Xie GY, Xia M, Miao YR, Luo M, Zhang Q, Guo AY.
FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human.
Bioinformatics. 2020 Apr 15;36(8):2605-2607. doi: 10.1093/bioinformatics/btz929. PMID: 31830251.

SEGtool 1.3 – Specifically Expressed Gene Detection

SEGtool 1.3

:: DESCRIPTION

SEGtool is an R package with self-adaptive function and high accuracy for specifically expressed gene (SEG, also known as tissue specific gene) detection.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

SEGtool

:: MORE INFORMATION

Citation

Zhang Q, Liu W, Liu C, Lin SY, Guo AY.
SEGtool: a specifically expressed gene detection tool and applications in human tissue and single-cell sequencing data.
Brief Bioinform. 2018 Nov 27;19(6):1325-1336. doi: 10.1093/bib/bbx074. PMID: 28981576.