TOBIAS 0.10.1 – Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal

TOBIAS 0.10.1

:: DESCRIPTION

TOBIAS is a framework of tools for investigating transcription factor binding from ATAC-seq signal

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

TOBIAS

:: MORE INFORMATION

Citation:

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation
Mette Bentsen, et al.
doi: https://doi.org/10.1101/869560

OLYMPUS – Hybrid Clustering method in Time Series Gene Expression

OLYMPUS

:: DESCRIPTION

OLYMPUS is an automated hybrid clustering method in the field of time series gene expression analysis.

::DEVELOPER

the Biosignal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 OLYMPUS

:: MORE INFORMATION

Citation

OLYMPUS: an automated hybrid clustering method in time series gene expression. Case study: host response after Influenza A (H1N1) infection.
Dimitrakopoulou K, Vrahatis AG, Wilk E, Tsakalidis AK, Bezerianos A.
Comput Methods Programs Biomed. 2013 Sep;111(3):650-61. doi: 10.1016/j.cmpb.2013.05.025.

WIlsON v2.3.1 – Webbased Interactive Omics visualizatioN

WIlsON v2.3.1

:: DESCRIPTION

The WIlsON R package employs the R Shiny and Plotly web-based frameworks using a client-server based approach comprising a range of interface and plotting modules.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

WIlsON

:: MORE INFORMATION

Citation:

Schultheis H, Kuenne C, Preussner J, Wiegandt R, Fust A, Bentsen M, Looso M.
WIlsON: Webbased Interactive Omics VisualizatioN.
Bioinformatics, 35 (6), 1055-1057 2019 Mar 15

UROPA 3.1.0 – Universal RObust Peak Annotation

UROPA 3.1.0

:: DESCRIPTION

UROPA is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature.

::DEVELOPER

the Loosolab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

UROPA

:: MORE INFORMATION

Citation:

Kondili M, Fust A, Preussner J, Kuenne C, Braun T, Looso M.
UROPA: a tool for Universal RObust Peak Annotation.
Scientific Reports. 2017;7:2593. doi:10.1038/s41598-017-02464-y.

bgmm 1.8.3 – Belief-based Gaussian Mixture Modeling

bgmm 1.8.3

:: DESCRIPTION

bgmm is an R package for knowledge-based mixture modeling. It implements mixture modeling variants, which differ with respect to the amount of incorporated knowledge, and spread the entire range from unsupervised to supervised modeling.

:: DEVELOPER

Vingron lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 bgmm

:: MORE INFORMATION

Citation

Introducing knowledge into differential expression analysis.
Szczurek E, Biecek P, Tiuryn J, Vingron M.
J Comput Biol. 2010 Aug;17(8):953-67. doi: 10.1089/cmb.2010.0034.

PDEGEM 20140325 – Modeling non-uniform Read Distribution in RNA-seq data

PDEGEM 20140325

:: DESCRIPTION

PDEGEM (Positional Dependent Energy Guided Expression Model ) is a robust nonlinear regression model to estimate the abundance of transcripts

::DEVELOPER

Minghua Deng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 PDEGEM

:: MORE INFORMATION

Citation

BMC Med Genomics. 2015 May 29;8 Suppl 2:S14. doi: 10.1186/1755-8794-8-S2-S14. Epub 2015 May 29.
PDEGEM: Modeling non-uniform read distribution in RNA-Seq data.
Xia Y, Wang F, Qian M, Qin Z, Deng M.

CCLasso – Correlation Inference for Compositional Data through Lasso

CCLasso

:: DESCRIPTION

CCLasso is a novel method based on least squares with ℓ1 penalty to infer the correlation network for latent variables of compositional data from metagenomic data

::DEVELOPER

Fang Huaying (hyfang@pku.edu.cn) , Minghua Deng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CCLasso

:: MORE INFORMATION

Citation

CCLasso: Correlation Inference for Compositional Data through Lasso.
Fang H, Huang C, Zhao H, Deng M.
Bioinformatics. 2015 Jun 4. pii: btv349.

MAìSTAS – Modeling and Assessment of ISoforms Through Automated Server

MAìSTAS

:: DESCRIPTION

Maìstas is a fully automatic pipeline aimed at building and assessing three-dimensional models for alternative splicing isoforms. The server builds, when possible, comparative structural models for all the splicing isoforms of a submitted gene or set of genes. The models are then analysed in terms of their suitability to exist in the monomeric state, i.e. when a warning appears in the model assessment, it cannot be excluded the possibility that other multimeric state may stabilize the structure.

::DEVELOPER

MAìSTAS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1625-9. doi: 10.1093/bioinformatics/btr198. Epub 2011 Apr 15.
MAISTAS: a tool for automatic structural evaluation of alternative splicing products.
Floris M1, Raimondo D, Leoni G, Orsini M, Marcatili P, Tramontano A.

DANCE 0.99.0 – Deregulation of Copy-number and Expression

DANCE 0.99.0

:: DESCRIPTION

DANCE quantifies the impact of copy-number alterations on gene expression and compares it between tumour sub-types.

::DEVELOPER

the Markowetz lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

 DANCE

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.
Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.
Yuan Y1, Rueda OM, Curtis C, Markowetz F.

openBIS 19.06.0/ openBIS ELN-LIMS – Managing Biological Information

openBIS 19.06.0 / openBIS ELN-LIMS

:: DESCRIPTION

openBIS is an open, distributed system for managing biological information. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata.

The aim of openBIS ELN-LIMS was to create a stable database with an intuitive and simple-to-use graphical user interface (GUI) where all relevant lab data can be collected.

::DEVELOPER

The Center for Information Sciences and Databases (CISD)

:: SCREENSHOTS

n/a

::REQUIREMENTS

  • Linux / Solaris / MacOS X
  • JRE
  • PostgreSQL

:: DOWNLOAD

  openBIS , openBIS ELN-LIMS

:: MORE INFORMATION

Citation

openBIS ELN-LIMS: an open-source database for academic laboratories.
Barillari C, Ottoz D, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F.
Bioinformatics. 2015 Oct 27. pii: btv606

BMC Bioinformatics. 2011 Dec 8;12:468. doi: 10.1186/1471-2105-12-468.
openBIS: a flexible framework for managing and analyzing complex data in biology research.
Bauch A, Adamczyk I, Buczek P, Elmer FJ, Enimanev K, Glyzewski P, Kohler M, Pylak T, Quandt A, Ramakrishnan C, Beisel C, Malmstr?m L, Aebersold R, Rinn B