scLVM 0.1 – Modelling framework for Single-cell RNA-seq data

scLVM 0.1

:: DESCRIPTION

scLVM (single-cell Latent Variable Model) is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Python
R

:: DOWNLOAD

scLVM

:: MORE INFORMATION

Citation

Nat Biotechnol. 2015 Feb;33(2):155-60. doi: 10.1038/nbt.3102. Epub 2015 Jan 19.
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O

starrynite II 20150713 – Accurate, Probabilistic Tracking for Single Cell analysis and understanding

starrynite II 20150713

:: DESCRIPTION

starrynite is an image analysis tool for tracking fluorescently-labeled nuclei during C. elegans embryogenesis.

::DEVELOPER

starrynite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows

:: DOWNLOAD

starrynite

:: MORE INFORMATION

Citation:

A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D,
Santella A, Du Z, Nowotschin S, Hadjantonakis AK and Bao Z
BMC Bioinformatics 2010, 11:580

PhISCS 1.0 – Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data

PhISCS 1.0

:: DESCRIPTION

PhISCS is a tool for sub-perfect tumor phylogeny reconstruction via integrative use of single cell and bulk sequencing data.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

PhISCS

:: MORE INFORMATION

Citation

Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC.
PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data.
Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18. PMID: 31628256; PMCID: PMC6836735.

ddClone – Joint Clustering of Single Cell and Bulk Data

ddClone

:: DESCRIPTION

A statistical framework leveraging data obtained from both single cell and bulk sequencing strategies. The ddClone is predicated on the notion that single cell sequencing data will inform and improve clustering of allele fractions derived from bulk sequencing data in a joint statistical model.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

ddClone

:: MORE INFORMATION

Citation

Genome Biol. 2017 Mar 1;18(1):44. doi: 10.1186/s13059-017-1169-3.
ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.
Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Côté A, Shah SP

CellScape 0.99.3 – Visualization tool for integrating single Cell Phylogeny

CellScape 0.99.3

:: DESCRIPTION

CellScape is a visualization tool for integrating single cell phylogeny with genomic content to clearly display evolutionary progression and tumour heterogeneity.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

CellScape

:: MORE INFORMATION

Sincell 1.24.0 – Analysis of Cell State Hierarchies from Single-cell RNA-seq

Sincell 1.24.0

:: DESCRIPTION

Sincell is an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.

::DEVELOPER

Miguel Juliá <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX
Python

:: DOWNLOAD

Sincell

:: MORE INFORMATION

Citation:

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.
Juliá M, Telenti A, Rausell A.
Bioinformatics. 2015 Jun 22. pii: btv368.

Vizardous 1.2.0 – Analysis of Microbial Populations with Single Cell Resolution

Vizardous 1.2.0

:: DESCRIPTION

Vizardous is a software for the visualization and evaluation of time-resolved, quantitative, single-cell data.

::DEVELOPER

Modeling & Simulation group at the IBG-1

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
Java

:: DOWNLOAD

Vizardous

:: MORE INFORMATION

Citation

Vizardous: interactive analysis of microbial populations with single cell resolution.
Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K.
Bioinformatics. 2015 Aug 10. pii: btv468

FiloDetect – Detect & Quantify Filopodia in Single-cell Fluorescence Confocal Microscopy Images

FiloDetect

:: DESCRIPTION

FiloDetect is an image analysis program for detecting and quantifying filopodia in single-cell fluorescence confocal microscopy images.

::DEVELOPER

Perkins Lab at the OHRI

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / MacOsX /Windows
MatLab

:: DOWNLOAD

FiloDetect

:: MORE INFORMATION

Citation

S. Nilufar, A. A. Morrow, J. M. Lee, T. J. Perkins
“FiloDetect: Automatic Detection of Filopodia from Fluorescence Microscopy Images”
BMC Syst Biol. 2013 Jul 23;7:66. doi: 10.1186/1752-0509-7-66.

GRM 0.2.1 – Single Cell RNA-seq De-noise Tools

GRM 0.2.1

:: DESCRIPTION

GRM is a powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.

::DEVELOPER

Wei Wang’s group

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

GRM

:: MORE INFORMATION

Citation

Normalization and noise reduction for single cell RNA-seq experiments.
Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, Wildberg A, Wang W.
Bioinformatics. 2015 Feb 24. pii: btv122.

CellTracer 1.0.3 – Automated Dynamic Image Analysis in Single Cell Fluorescent Microscopy studies

CellTracer 1.0.3

:: DESCRIPTION

CellTracer is an integrated graphical user interface written in Matlab that implements a few novel methods for automating cell segmentation/lineage reconstruction. It is designed for biologists without training in image processing or programing to extract single cell information from microscopy images arising in their studies.

::DEVELOPER

Mike West

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Matlab

:: DOWNLOAD

CellTracer

:: MORE INFORMATION

Citation

CellTracer: Software for automated image segmentation and lineage mapping for single-cell studies,
Quanli Wang, Lingchong You and Mike West.