Tag: Analysis Pipeline

Tilescope 2.0 – Online Analysis Pipeline for High-density Tiling Microarray data

Tilescope 2.0

:: DESCRIPTION

Tilescope is a fully integrated data processing pipeline for analyzing tiling array data. In a completely automated fashion, it will normalize signals between channels and across arrays, combine replicate experiments, score each array element, and identify genomic features.

::DEVELOPER

ZDZ lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows / MacOsX
  • Java

:: DOWNLOAD

 Tilescope

:: MORE INFORMATION

Citation

Genome Biol. 2007;8(5):R81.
Tilescope: online analysis pipeline for high-density tiling microarray data.
Zhang ZD1, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M.

mit-o-matic – Automated Mitochondrial Variation Analysis Pipeline

mit-o-matic

:: DESCRIPTION

mit-o-matic is a tool designed to provide clinically relevant information distributed in disparate resources for understanding and annotating mtDNA variations.

::DEVELOPER

Dr. Vinod Scaria Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hum Mutat. 2015 Feb 11. doi: 10.1002/humu.22767.
mit-o-matic: A comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets.
Vellarikkal SK1, Dhiman H, Joshi K, Hasija Y, Sivasubbu S, Scaria V.

COHCAP 1.38.0 – City of Hope CpG Island Analysis Pipeline

COHCAP 1.38.0

:: DESCRIPTION

COHCAP is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). It provides QC metrics, differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, and visualization of methylation values.

::DEVELOPER

Charles Warden <cwarden45 at gmail.com>

:: SCREENSHOTS

COHCAP

:: REQUIREMENTS

  • Windows/ Linux/MacOsX
  • JRE/ R

:: DOWNLOAD

 COHCAP

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jun;41(11):e117. doi: 10.1093/nar/gkt242
COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.
Warden CD1, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC.

MOTIPS – Motif Analysis Pipeline

MOTIPS

:: DESCRIPTION

MOTIPS employs an efficient search algorithm to scan a target proteome for potential domain targets and to increase the accuracy of each hit by integrating a variety of pre-computed features, such as conservation, surface propensity, and disorder.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server
  • Java

:: DOWNLOAD

MOTIPS 

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 May 11;11:243. doi: 10.1186/1471-2105-11-243.
MOTIPS: automated motif analysis for predicting targets of modular protein domains.
Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB.

SC1 – A web-based Single Cell RNA-seq Analysis Pipeline

SC1

:: DESCRIPTION

SC1 is a web-based single cell RNA-seq analysis pipeline.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

J Comput Biol. 2019 Aug;26(8):822-835. doi: 10.1089/cmb.2018.0236. Epub 2019 Feb 19.
Locality Sensitive Imputation for Single Cell RNA-Seq Data.
Moussa M, Măndoiu II.

Mercury 3.2.1 – Next Generation Sequence Analysis Pipeline

Mercury 3.2.1

:: DESCRIPTION

Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Valence
  • Perl
  • Python

:: DOWNLOAD

Mercury

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 29;15:30. doi: 10.1186/1471-2105-15-30.
Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.
Reid JG1, Carroll A, Veeraraghavan N, Dahdouli M, Sundquist A, English A, Bainbridge M, White S, Salerno W, Buhay C, Yu F, Muzny D, Daly R, Duyk G, Gibbs RA, Boerwinkle E.

MethPipe 3.4.3 – DNA Methylation Data Analysis Pipeline

MethPipe 3.4.3

:: DESCRIPTION

The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS).

::DEVELOPER

The Smith Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MethPipe

:: MORE INFORMATION

Citation

Song Qiang, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD.
A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics.
PloS one 8.12 (2013): e81148.