GSCA / GSCALite – Gene Set Cancer Analysis

GSCA / GSCALite

:: DESCRIPTION

GSCA is an integrated database for genomic and immunogenomic gene set cancer analysis.

GSCALite is a web-based analysis platform for gene set cancer analysis. The alterations on DNA or RNA of cancer related genes may be contribute to the cancer initiation, progress, diagnosis, prognosis, therapy. As the cancer genomics big data available, it is very useful and urgent to provide a platform for gene set analysis in cancer.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Liu CJ, Hu FF, Xia MX, Han L, Zhang Q, Guo AY.
GSCALite: a web server for gene set cancer analysis.
Bioinformatics. 2018 Nov 1;34(21):3771-3772. doi: 10.1093/bioinformatics/bty411. PMID: 29790900.

GEDS – Gene Expression Display Server

GEDS

:: DESCRIPTION

GEDS is an integrative platform to show human gene expressions in cancer types, normal tissues and cell lines for user input genes, miRNAs and proteins.

::DEVELOPER

An-Yuan Guo’s Bioinformatics Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Xia M, Liu CJ, Zhang Q, Guo AY.
GEDS: A Gene Expression Display Server for mRNAs, miRNAs and Proteins.
Cells. 2019 Jul 3;8(7):675. doi: 10.3390/cells8070675. PMID: 31277321; PMCID: PMC6678772.

Tronco v2.26.0 – Inference of Cancer Progression Models

Tronco v2.26.0

:: DESCRIPTION

Tronco (TRONCO TRanslational ONCOlogy)is an R suite for state-of-the-art algorithms for the reconstruction of causal models of cancer progressions from genomic cross-sectional data.

::DEVELOPER

Data and Computational Biology @ University of Milan – Bicocca.

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/windows/MacOsX
R
BioConductor
rgraphviz

:: DOWNLOAD

Tronco

:: MORE INFORMATION

Citation

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.
De Sano L, Caravagna G, Ramazzotti D, Graudenzi A, Mauri G, Mishra B, Antoniotti M.
Bioinformatics. 2016 Feb 9. pii: btw035.

CAPRI: Efficient Inference of Cancer Progression Models from Cross-sectional Data.
Ramazzotti D, Caravagna G, Olde-Loohuis L, Graudenzi A, Korsunsky I, Mauri G, Antoniotti M, Mishra B.
Bioinformatics. 2015 May 13. pii: btv296.

nextNEOpi v1.2 – NeoEpitope predictions Nextflow Pipeline

nextNEOpi v1.2

:: DESCRIPTION

nextNEOpi is a comprehensive pipeline for computational neoantigen prediction.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

nextNEOpi

:: MORE INFORMATION

Citation

Rieder D, Fotakis G, Ausserhofer M, René G, Paster W, Trajanoski Z, Finotello F.
nextNEOpi: a comprehensive pipeline for computational neoantigen prediction.
Bioinformatics. 2021 Nov 12:btab759. doi: 10.1093/bioinformatics/btab759. Epub ahead of print. PMID: 34788790.

pdCSM-PPI – Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors

pdCSM-PPI

:: DESCRIPTION

pdCSM-PPI is a machine learning approach that uses a graph-based representation of small molecules to guide identification of inhibitors modulating protein-protein interactions.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Rodrigues CHM, Pires DEV, Ascher DB.
pdCSM-PPI: Using Graph-Based Signatures to Identify Protein-Protein Interaction Inhibitors.
J Chem Inf Model. 2021 Nov 22;61(11):5438-5445. doi: 10.1021/acs.jcim.1c01135. Epub 2021 Nov 1. PMID: 34719929.

mmCSM-NA – Predicting Effects of Single and Multiple Mutations on Protein-nucleic Acid Binding affinity

mmCSM-NA

:: DESCRIPTION

mmCSM-NA is the first scalable method capable of quantitatively and accurately predicting the effects of multiple-point mutations on nucleic acid binding affinities.

::DEVELOPER

Biosig Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nguyen TB, Myung Y, de Sá AGC, Pires DEV, Ascher DB.
mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity.
NAR Genom Bioinform. 2021 Nov 17;3(4):lqab109. doi: 10.1093/nargab/lqab109. PMID: 34805992; PMCID: PMC8600011.

CoRe v1.0.2 – Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens

CoRe v1.0.2

:: DESCRIPTION

CoRe is an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens.

::DEVELOPER

CoRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

CoRe

:: MORE INFORMATION

Citation

Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
BMC Genomics. 2021 Nov 17;22(1):828. doi: 10.1186/s12864-021-08129-5. PMID: 34789150.

PsRRR – Pathways Sparse Reduced Rank Regression

PsRRR

:: DESCRIPTION

PsRRR is a method for detecting gene pathways associated with a multivariate quantitative trait or phenotype.

::DEVELOPER

PsRRR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Python

:: DOWNLOAD

PsRRR

:: MORE INFORMATION

Citation

Neuroimage. 2012 Nov 15;63(3):1681-94. doi: 10.1016/j.neuroimage.2012.08.002. Epub 2012 Aug 15.
Identification of gene pathways implicated in Alzheimer’s disease using longitudinal imaging phenotypes with sparse regression.
Silver M1, Janousova E, Hua X, Thompson PM, Montana G; Alzheimer’s Disease Neuroimaging Initiative.

AutoClickChem 1.0.0 – Performing Click-chemistry Reactions in silico

AutoClickChem 1.0.0

:: DESCRIPTION

AutoclickChem is a computer program capable of performing click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compounds for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

::DEVELOPER

APBS Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

AutoClickChem

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012;8(3):e1002397. doi: 10.1371/journal.pcbi.1002397. Epub 2012 Mar 15.
AutoClickChem: click chemistry in silico.
Durrant JD1, McCammon JA.

TagGD – DNA Tag Generation and Demultiplexing

TagGD

:: DESCRIPTION

TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy.

::DEVELOPER

the Science for Life Laboratory, Uppsala University,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX/Windows

:: DOWNLOAD

TagGD

:: MORE INFORMATION

Citation

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.
TagGD: fast and accurate software for DNA Tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.