CELLector v1.2.1 – Genomics Guided Selection of Cancer in Vitro Models

CELLector v1.2.1

:: DESCRIPTION

CELLector is a computational tool for selecting the most clinically relevant cancer cell lines to be included in a new in-vitro study (or to be considered in a retrospective study), in a patient-genomic guided fashion.

::DEVELOPER

Cancer Dependency Map Analytics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

CELLector

:: MORE INFORMATION

Citation

Najgebauer H, Yang M, Francies HE, Pacini C, Stronach EA, Garnett MJ, Saez-Rodriguez J, Iorio F.
CELLector: Genomics-Guided Selection of Cancer In Vitro Models.
Cell Syst. 2020 May 20;10(5):424-432.e6. doi: 10.1016/j.cels.2020.04.007. PMID: 32437684.

EDGAR 3.0 – software platform for comparative Genomics

EDGAR 3.0

:: DESCRIPTION

EDGAR (Efficient Database framework for comparative Genome Analyses using BLAST score Ratios) is designed to automatically perform genome comparisons in a high throughput approach.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Dieckmann MA, Beyvers S, Nkouamedjo-Fankep RC, Hanel PHG, Jelonek L, Blom J, Goesmann A.
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure.
Nucleic Acids Res. 2021 Jul 2;49(W1):W185-W192. doi: 10.1093/nar/gkab341. PMID: 33988716; PMCID: PMC8262741.

EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Pühler A, Vorh?lter FJ, Zakrzewski M, Goesmann A.
BMC Bioinformatics. 2009 May 20;10:154. doi: 10.1186/1471-2105-10-154.

ORCA – Genomics Research Container Architecture

ORCA

:: DESCRIPTION

ORCA is a platform for bioinformatics analysis. It is suited for those wishing to conduct self-serve analysis using their own existing data. Hundreds of bioinformatics tools from Brewsci/bio are installed in the ORCA Docker image using Linuxbrew.

::DEVELOPER

BC Cancer Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Docker

:: DOWNLOAD

ORCA

:: MORE INFORMATION

Citation

Jackman SD, Mozgacheva T, Chen S, O’Huiginn B, Bailey L, Birol I, Jones SJM.
ORCA: a comprehensive bioinformatics container environment for education and research.
Bioinformatics. 2019 Nov 1;35(21):4448-4450. doi: 10.1093/bioinformatics/btz278. PMID: 31004474; PMCID: PMC6821186.

PiGx v0.0.3 – Pipelines in Genomics

PiGx v0.0.3

:: DESCRIPTION

PiGx is a collection of genomics pipelines. All pipelines are easily configured with a simple sample sheet and a descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PiGx

:: MORE INFORMATION

Citation

Wurmus R, Uyar B, Osberg B, Franke V, Gosdschan A, Wreczycka K, Ronen J, Akalin A.
PiGx: reproducible genomics analysis pipelines with GNU Guix.
Gigascience. 2018 Dec 1;7(12):giy123. doi: 10.1093/gigascience/giy123. PMID: 30277498; PMCID: PMC6275446.

GenomeVX – Bioinformatics Solution towards the field of Genomics

GenomeVX

:: DESCRIPTION

GenomeVX is a bioinformatics solution towards the field of Genomics. GenomeVX helps in understanding Genome-wide comparative analyses of different human populations, as well as between species, focusing on association studies relating genetic variation to disease with evidence of mutations. GenomeVX extracts data from the fields in VCF file (generated by the Genome 1000 Browser) and displays alleles for the substitutions and variations (SNP).

::DEVELOPER

DEPARTMENT OF NEUROBIOLOGY & GENETICS, Biocenter, Universit of Wuerzburg

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

GenomeVX

:: MORE INFORMATION

TeachEnG – Teaching Engine for Genomics

TeachEnG

:: DESCRIPTION

TeachEnG provides interactive modules to help students and researchers understand key bioinformatics concepts. The current version includes sequence alignment and phylogenetic tree reconstruction algorithms, with selective tutorials.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

TeachEnG

:: MORE INFORMATION

Citation

Kim M, Kim Y, Qian L, Song JS.
TeachEnG: a Teaching Engine for Genomics.
Bioinformatics. 2017 Oct 15;33(20):3296-3298. doi: 10.1093/bioinformatics/btx447. PMID: 29028264; PMCID: PMC5860038.

Kraken 1.0 – Genomic Coordinate Translator for Comparative Genomics

Kraken 1.0

:: DESCRIPTION

Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings.

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Compiler

:: DOWNLOAD

Kraken

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 30;15:227. doi: 10.1186/1471-2105-15-227.
A universal genomic coordinate translator for comparative genomics.
Zamani N1, Sundström G, Meadows JR, Höppner MP, Dainat J, Lantz H, Haas BJ, Grabherr MG.

Hetero-RP – Enhanced Clustering and Classification in Integrative Genomics

Hetero-RP

:: DESCRIPTION

Hetero-RP (Heterogeneity Rescaling Pursuit) is a scalable and tuning-free preprocessing framework, which weighs important features more highly than less important ones in accord with implicitly existing auxiliary knowledge.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Python

:: DOWNLOAD

Hetero-RP

:: MORE INFORMATION

Citation

Lu YY, Lv J, Fuhrman JA, Sun F.
Towards enhanced and interpretable clustering/classification in integrative genomics.
Nucleic Acids Res. 2017 Nov 16;45(20):e169. doi: 10.1093/nar/gkx767. PMID: 28977511; PMCID: PMC5714251.

EggLib 3.0.0 – C++/Python library and program package for Evolutionary Genetics and Genomics

EggLib 3.0.0

:: DESCRIPTION

EggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features are sequence data management, sequence polymorphism analysis, coalescent simulations and Approximate Bayesian Computation.

::DEVELOPER

EggLib team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / MacOsX
Python/C++ Compiler

:: DOWNLOAD

EggLib

:: MORE INFORMATION

Citation

De Mita S. and M. Siol. 2012.
EggLib: processing, analysis and simulation tools for population genetics and genomics.
BMC Genet. 13:27.

Copy Number Explorer 1.3 – Interactive Copy Number Analysis for Cancer Genomics

Copy Number Explorer 1.3

:: DESCRIPTION

Copy Number Explorer is a data mining tool for cancer researchers interested in the structural and copy number changes.

Copy Number Explorer online version

::DEVELOPER

Scott Newman, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
Perl

:: DOWNLOAD

Copy Number Explorer

:: MORE INFORMATION

Citation

Interactive analysis of large cancer copy number studies with Copy Number Explorer.
Newman S.
Bioinformatics. 2015 May 7. pii: btv298.