CRISPRitz – Perform in-silico CRISPR analysis and Assessment

CRISPRitz

:: DESCRIPTION

CRISPRitz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux
Conda

:: DOWNLOAD

CRISPRitz

:: MORE INFORMATION

Citation

Cancellieri S, Canver MC, Bombieri N, Giugno R, Pinello L.
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing.
Bioinformatics. 2020 Apr 1;36(7):2001-2008. doi: 10.1093/bioinformatics/btz867. PMID: 31764961; PMCID: PMC7141852.

Sylamer 1.0 – Fast Assessment of microRNA Binding and siRNA off-target effects from Expression data

Sylamer 1.0

:: DESCRIPTION

Sylamer is a system for finding significantly over or under-represented words in sequences according to a sorted gene list. Typically it is used to find significant enrichment or depletion of microRNA or siRNA seed sequences from microarray expression data. Sylamer is extremely fast and can be applied to genome-wide datasets with ease. Results are plotted in terms of a significance landscape plot. These plots show significance profiles for each word studied across the sorted genelist.

::DEVELOPER

Stijn van Dongen

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux
Java / R package / C Compiler

:: DOWNLOAD

Sylamer

:: MORE INFORMATION

Citation

Stijn van Dongen, Cei Abreu-Goodger & Anton J. Enright;
Detecting microRNA binding and siRNA off-target effects from expression data
Nat Methods. 2008 December; 5(12): 1023–1025.

MuSERA v.2.3 – Multiple Sample Enriched Region Assessment

MuSERA v.2.3

:: DESCRIPTION

MuSERA is a tool that optimally implements multiple-sample enriched region analysis, with a user-friendly graphical interface.

::DEVELOPER

MuSERA team

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows

:: DOWNLOAD

MuSERA

:: MORE INFORMATION

Citation

Jalili V, Matteucci M, Morelli MJ, Masseroli M.
MuSERA: Multiple Sample Enriched Region Assessment.
Brief Bioinform. 2017 May 1;18(3):367-381. doi: 10.1093/bib/bbw029. PMID: 27013647.

Coala 1.2.1 – COevolution Assessment by a Likelihood-free Approach

Coala 1.2.1

:: DESCRIPTION

Coala is an algorithm for estimating the frequency of the events based on an approximate Bayesian computation approach.

::DEVELOPER

ERABLE (European Research team in Algorithms and Biology, formaL and Experimental)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
Java

:: DOWNLOAD

Coala

:: MORE INFORMATION

Citation

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier, C. Matias, and M.-F. Sagot.
Cophylogeny reconstruction via an approximate Bayesian computation.
Systematic Biology, 2014, doi:10.1093/sysbio/syu129.

BIGpre 2.0.2 – Quality Assessment software for both Illumina and 454 platforms

BIGpre 2.0.2

:: DESCRIPTION

BIGpre is a quality assessment package for next-genomics sequencing data

::DEVELOPER

BIGpre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BIGpre

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.
BIGpre: a quality assessment package for next-generation sequencing data.
Zhang T1, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

JACUSA v2.0.2-RC – JAVA framework for accurate SNV Assessment

JACUSA v2.0.2-RC

:: DESCRIPTION

JACUSA2 is a one-stop solution to detect single nucleotide variants (SNVs) and reverse transcriptase induced arrest events in Next-generation sequencing (NGS) data.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
Jav

:: DOWNLOAD

JACUSA2

:: MORE INFORMATION

Citation.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C.
JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
BMC Bioinformatics. 2017 Jan 3;18(1):7. doi: 10.1186/s12859-016-1432-8. PMID: 28049429; PMCID: PMC5210316.

ClassifyR 2.12.0 – Performance Assessment of Classification with Applications to Transcriptomics

ClassifyR 2.12.0

:: DESCRIPTION

ClassifyR is a framework for two-class classification problems, with applications to differential variability and differential distribution testing.

::DEVELOPER

Dario Strbenac <dario.strbenac at sydney.edu.au>, John Ormerod, Graham Mann, Jean Yang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R
BioConductor

:: DOWNLOAD

ClassifyR

:: MORE INFORMATION

Citation

ClassifyR: An R Package for Performance Assessment of Classification with Applications to Transcriptomics.
Strbenac D, Mann GJ, Ormerod JT, Yang JY.
Bioinformatics. 2015 Feb 1. pii: btv066.

ClusterA 1004 – Calculating Silhouette scores for Assessment of SNP Genotype Clusters

ClusterA 1004

:: DESCRIPTION

ClusterA is a tool for calculating some statistics on clusters, the most important being the “Silhouette Score” used in our group for genotype cluster validation.

::DEVELOPER

Molecular Medicine research group

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

ClusterA

:: MORE INFORMATION

Citation

Lovmar L, Ahlford A, Jonsson M, Syvänen A-C (2005)
Silhouette scores for assessment of SNP genotype clusters.
BMC Genomics 6:35

MRMPlusGUI 20151104 – Quality Control and Assessment tool for SRM/MRM Assay development

MRMPlusGUI 20151104

:: DESCRIPTION

MRMPlusGUI is a freely available, open-source tool in the platform independent Java programming language to compute analytical measures as recommended recently by the Clinical Proteomics Tumor Analysis Consortium Assay Development Working Group for “Tier 2” assays.

::DEVELOPER

MRMPlusGUI team

:: SCREENSHOTS

:: REQUIREMENTS

MacOsX/Linux / Windows
Java

:: DOWNLOAD

MRMPlusGUI

:: MORE INFORMATION

Citation

MRMPlus: an open source quality control and assessment tool for SRM/MRM assay development.
Aiyetan P, Thomas SN, Zhang Z, Zhang H.
BMC Bioinformatics. 2015 Dec 12;16(1):411. doi: 10.1186/s12859-015-0838-z.

BIDDSAT 0.3 – BIoDiversity DataSet Assessment Tool

BIDDSAT 0.3

:: DESCRIPTION

BIDDSAT is an online tool that enables selected diagnostic visualizations on the content of data publishers and/or their individual collections.

::DEVELOPER

Javier Otegui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser
PHP

:: DOWNLOAD

BIDDSAT

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 15;28(16):2207-8. doi: 10.1093/bioinformatics/bts359. Epub 2012 Jun 23.
BIDDSAT: visualizing the content of biodiversity data publishers in the Global Biodiversity Information Facility network.
Otegui J, Ariño AH.