FIATAS 1.0 – Fast Image AnnoTAtion Software

FIATAS 1.0

:: DESCRIPTION

FIATAS is used for assay annotation . The annotation tool has been developed with the idea that the editor/annotators are presented with the set of images associated with a single assay to be annotated, and an optimized anatomy ontology so the expert user can rapidly assign annotations to a given image set. Each image in the set can be independently annotated in terms of tissues/structures that show expression and the nature, strength and patterning of that expression. Comments can be added to any annotation as well as a general comment on the whole set.

::DEVELOPER

Eurexpress project

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 FIATAS

:: MORE INFORMATION

MAGI – Mutation Annotation & Genome Interpretation

MAGI

:: DESCRIPTION

MAGI is a publicly available web application to explore and annotate cancer genomics data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

MAGI

:: MORE INFORMATION

Citation:

MAGI: visualization and collaborative annotation of genomic aberrations.
Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ.
Nat Methods. 2015 May 28;12(6):483-4. doi: 10.1038/nmeth.3412.

COFACTOR – Structure-based Protein Function Annotation

COFACTOR

:: DESCRIPTION

COFACTOR is a structure-based method for biological function annotation of protein molecules.

::DEVELOPER

Yang Zhang’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W471-7. doi: 10.1093/nar/gks372. Epub 2012 May 8.
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.
Roy A1, Yang J, Zhang Y.

OsCAS – Annotation platform for Rice Microarray data

OsCAS

:: DESCRIPTION

OsCAS (Oryza sativa Chips Annotation System) is a comprehensive system designed to annotate the results of rice microarray experiments and analysis relationships between genes based on their expression. The aim of the platform is to facilitate the study of differently expressed genes in the microarray experiments within the framework of systems biological research.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Qingyun Shi, Yijun Meng, Dijun Chen, Fei He, Haibin Gu, Ping Wu, Ming Chen(2010)
OsCAS: a comprehensive web-based annotation platform for rice microarray data.
BioChip Journal, 4(1): 9-15.

URSAHD – Unveiling RNA Sample Annotation for Human Diseases

URSAHD

:: DESCRIPTION

URSA (Unveiling RNA Sample Annotation), originally released in 2013, simultaneously estimated the probabilities that a given sample is associated with a particular tissue or cell-type. Individual cell-type models were constructed from more than ten thousand manually curated samples from GEO and then aggregated using Bayesian Correction. This method has been shown effective for both array-based and sequence-based genome-scale experiments.

::DEVELOPER

Troyanskaya Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Lee YS, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, Kristensen VN, Dolinski K, Theesfeld CL, Troyanskaya OG.
A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.
Cell Syst. 2019 Feb 27;8(2):152-162.e6. doi: 10.1016/j.cels.2018.12.010. Epub 2019 Jan 23. PMID: 30685436; PMCID: PMC7374759.

RefLnc – comprehensive Annotation for human long noncoding RNAs(lncRNAs)

RefLnc

:: DESCRIPTION

RefLnc is a comprehensive annotation for human long noncoding RNAs(lncRNAs).Each lncRNA in the atlas is characterized by a panorama of sequence, expression and trait association.

::DEVELOPER

Gao Lab, Peking University.

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • R

:: DOWNLOAD

RefLnc

:: MORE INFORMATION

Citation

Jiang S, Cheng SJ, Ren LC, Wang Q, Kang YJ, Ding Y, Hou M, Yang XX, Lin Y, Liang N, Gao G.
An expanded landscape of human long noncoding RNA.
Nucleic Acids Res. 2019 Sep 5;47(15):7842-7856. doi: 10.1093/nar/gkz621. PMID: 31350901; PMCID: PMC6735957.

GFam 1.4 – Gene Family Annotation & Maintenance

GFam 1.4

:: DESCRIPTION

GFam is a command-line tool for automatic annotation of gene families. GFam offers a framework for complete genome initiatives and model organism resources to build domain-based gene families, derive meaningful functional labels and maintain family annotation across genome releases seamlessly. Our approach achieves a unified system for grouping proteins based on evolutionary and functional relationships.

::DEVELOPER

Paccanaro Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 GFam

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Oct;40(19):e152. doi: 10.1093/nar/gks631. Epub 2012 Jul 11.
GFam: a platform for automatic annotation of gene families.
Sasidharan R1, Nepusz T, Swarbreck D, Huala E, Paccanaro A.

Workflow4Metabolomics 4.0 – Metabolomics data Processing, Analysis and Annotation

Workflow4Metabolomics 4.0

:: DESCRIPTION

Workflow4Metabolomics (W4M) is a first fully open-source and collaborative online platform for computational metabolomics.

::DEVELOPER

Workflow4Metabolomics team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/Oracle/virtual machines (VM)

:: DOWNLOAD

 Workflow4Metabolomics

:: MORE INFORMATION

Citation

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.
Giacomoni F, Le Corguillé G, Monsoor M, Landi M, Pericard P, Pétéra M, Duperier C, Tremblay-Franco M, Martin JF, Jacob D, Goulitquer S, Thévenot EA, Caron C.
Bioinformatics. 2014 Dec 19. pii: btu813.

VariantAnnotation 1.36.0 – Annotation of Genetic Variants

VariantAnnotation 1.36.0

:: DESCRIPTION

VariantAnnotation is an R / Bioconductor package for the exploration and annotation of genetic variants. Capabilities exist for reading, writing and filtering variant call format (VCF) files

::DEVELOPER

VariantAnnotation team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 VariantAnnotation

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Apr 21. [Epub ahead of print]
VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants.
Obenchain V, Lawrence M, Carey V, Gogarten S, Shannon P, Morgan M.