EditR 1.0.8 / MultiEditR 1.1.0 – Multiple Edit Deconvolution by Inference of Traces in R

EditR 1.0.8 / MultiEditR 1.1.0

:: DESCRIPTION

EditR is an algorithm for simple and cost effective measurement of base editing by quantifying Sanger trace fluorescence

MultiEditR is an easy validation method for detecting and quantifying RNA editing from Sanger sequencing.

::DEVELOPER

Moriarity Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

EditR , MultiEditR

:: MORE INFORMATION

Citation

Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS.
EditR: A Method to Quantify Base Editing from Sanger Sequencing.
CRISPR J. 2018 Jun;1(3):239-250. doi: 10.1089/crispr.2018.0014. PMID: 31021262; PMCID: PMC6694769.

Kluesner MG, Tasakis RN, Lerner T, Arnold A, Wüst S, Binder M, Webber BR, Moriarity BS, Pecori R.
MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq.
Mol Ther Nucleic Acids. 2021 Jul 21;25:515-523. doi: 10.1016/j.omtn.2021.07.008. PMID: 34589274; PMCID: PMC8463291.

MetaboliteDetector 3.3 – Deconvolution and Analysis of GC/MS Data

MetaboliteDetector 3.3

:: DESCRIPTION

Metabolite Detector is a QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments.

::DEVELOPER

MetaboliteDetector Team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows

:: DOWNLOAD

MetaboliteDetector

:: MORE INFORMATION

Citation

Anal Chem. 2009 May 1;81(9):3429-39. doi: 10.1021/ac802689c.
MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis.
Hiller K, Hangebrauk J, J?ger C, Spura J, Schreiber K, Schomburg D.

CellMix 1.6.2 – Gene Expression Deconvolution

CellMix 1.6.2

:: DESCRIPTION

CellMix , an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

::DEVELOPER

The UCT Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX/ Windows
R package

:: DOWNLOAD

CellMix

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.
CellMix: a comprehensive toolbox for gene expression deconvolution.
Gaujoux R1, Seoighe C.

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows /Linux/ MacOsX

:: DOWNLOAD

HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.

UNDO 1.34.0 – Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

UNDO 1.34.0

:: DESCRIPTION

UNDO (UNsupervised DecOnvolution) is an R package that can be used to automatically detect cell-specific marker genes located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample, and deconvolute mixed expressions into cell-specific expression profiles.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R
Bioconductor

:: DOWNLOAD

UNDO

:: MORE INFORMATION

Citation

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.
Wang N, Gong T, Clarke R, Chen L, Shih IM, Zhang Z, Levine DA, Xuan J, Wang Y.
Bioinformatics. 2015 Jan 1;31(1):137-9. doi: 10.1093/bioinformatics/btu607.

CRISPRCloud2 – Deconvolution of your CRISPR pooled screening data

CRISPRCloud2

:: DESCRIPTION

CRISPRCloud2 is a user-friendly cloud-based analysis platform for the deconvolution of CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats) pooled screening data.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Jeong HH, Kim SY, Rousseaux MWC, Zoghbi HY, Liu Z.
CRISPRcloud: a secure cloud-based pipeline for CRISPR pooled screen deconvolution.
Bioinformatics. 2017 Sep 15;33(18):2963-2965. doi: 10.1093/bioinformatics/btx335. PMID: 28541456; PMCID: PMC5870715.

PERT 1.0 – Expression Deconvolution under Varied Environmental Conditions

PERT 1.0

:: DESCRIPTION

The PERT algorithm is designed for expression deconvolution of samples of mixed cell types, where the expression profiles of most of the individual cell types are available and we simply want to estimate the proportion of each mixed sample that is attributable to each individual cell type.

::DEVELOPER

QUON-TITATIVE BIOLOGY LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /
Octave

:: DOWNLOAD

PERT

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012;8(12):e1002838. doi: 10.1371/journal.pcbi.1002838. Epub 2012 Dec 20.
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.
Qiao W1, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.

ISOpure 1.0 / ISOpureR 1.1.3 – Gene Expression Deconvolution and Purification

ISOpure 1.0 / ISOpureR 1.1.3

:: DESCRIPTION

ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample, and an estimate of the proportion of RNA originating from cancerous cells.

ISOpureR: Deconvolution of Tumour Profiles

::DEVELOPER

QUON-TITATIVE BIOLOGY LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
MatLab / R

:: DOWNLOAD

ISOpure , ISOpureR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.
Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC

Genome Med. 2013 Mar 28;5(3):29.
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.
Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.

MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package

:: DOWNLOAD

MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

tracy v0.5.9 – Basecalling, Alignment, Assembly and Deconvolution of Sanger Chromatogram trace files

tracy v0.5.9

:: DESCRIPTION

Tracy is an efficient and versatile command-line application that enables basecalling, alignment, assembly and deconvolution of sequencing chromatogram files.

::DEVELOPER

Tobias Rausch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / OsX
Bioconda package

:: DOWNLOAD

Tracy

:: MORE INFORMATION

Citation:

Rausch T, Fritz MH, Untergasser A, Benes V.
Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files.
BMC Genomics. 2020 Mar 14;21(1):230. doi: 10.1186/s12864-020-6635-8. PMID: 32171249; PMCID: PMC7071639.