Category: Cytometry / Cell

FCS Express 7.06.0015 – Flow Cytometry Tool

FCS Express 7.06.0015

:: DESCRIPTION

FCS Express can rapidly analyze vast amounts of data, with industry leading flow cytometry tools, but we recognize that is only the beginning of the scientific journey. After the basic analysis is complete, you must compile spreadsheets comparing your data to previous experiments, create bar charts and scatter plots to show these differences and create presentations to show your work to others. FCS Express seamlessly takes you from your primary listmode data files to flexible overviews of your entire experiment.

::DEVELOPER

DE NOVO SOFTWARE

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

FCS Express

:: MORE INFORMATION

WEASEL 3.7.1 – Flow Cytometry Data Analysis

WEASEL 3.7.1

:: DESCRIPTION

WEASEL is a general purpose flow cytometry data analysis and display program developed at WEHI. As can be seen from the sample screen below, many different display formats are possible as are the extraction of a number of numerical or statistical measures. Multiple flow cytometry standard (FCS) data files can be compared side-by-side on screen and there is facility for fast scanning through collections of data files. Display layouts may be saved as may high quality graphics which may be incorporated into other documents. One of the program’s design parameters was to make operation as simple and intuitive as possible so self instruction should be the best course.

::DEVELOPER

Frank Battye PhD

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX /  Linux
  • Java

:: DOWNLOAD

WEASEL

:: MORE INFORMATION

flowPeaks 1.38.0 – Fast unsupervised Clustering for Flow Cytometry Data

flowPeaks 1.38.0

:: DESCRIPTION

flowPeaks is a fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means

::DEVELOPER

Yongchao Ge<yongchao.ge at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • BioConductor/ R

:: DOWNLOAD

 flowPeaks

:: MORE INFORMATION

Citation

flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding.
Ge Y, Sealfon SC.
Bioinformatics. 2012 Aug 1;28(15):2052-8. doi: 10.1093/bioinformatics/bts300

flowBin 1.28.0 – Combining Multitube Flow Cytometry data by Binning

flowBin 1.28.0

:: DESCRIPTION

flowBin is a parameterisation-free method for combining multitube flow cytometry data into a higher-dimensional form suitable for deep profiling and discovery.

::DEVELOPER

Kieran O’Neill <koneill at bccrc.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOs
  • R
  • Bioconductor

:: DOWNLOAD

 flowBin

:: MORE INFORMATION

Citation

Deep profiling of multitube flow cytometry data.
O’Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR.
Bioinformatics. 2015 Jan 18. pii: btv008.

Mogrify – A Directory of defined Factors for direct Cell Reprogramming

Mogrify

:: DESCRIPTION

Mogrify uses a network-based algorithm designed to find transcription factors that impart the most influence on changes in cellular state. This website will allow you to explore possible reprogramming experiments, different collections of transcription factors as well as the look at the changes in the regulatory network.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

::  REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Owen J L Rackham, et al.
A predictive computational framework for direct reprogramming between human cell types
Nat Genet. 2016 Mar;48(3):331-5. doi: 10.1038/ng.3487.

CellNet / CellNetR – Network Biology applied to Stem Cell Engineering

CellNet / CellNetR

:: DESCRIPTION

CellNet is a network biology-based computational platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations.

::DEVELOPER

Hu Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Max OS X
  • R

:: DOWNLOAD

 CellNetR

:: MORE INFORMATION

Citation:

CellNet: network biology applied to stem cell engineering.
Cahan P, Li H, Morris SA, Lummertz da Rocha E, Daley GQ, Collins JJ.
Cell. 2014 Aug 14;158(4):903-15. doi: 10.1016/j.cell.2014.07.020.

scHiCNorm – Eliminate Systematic Biases in Single-cell Hi-C data

scHiCNorm

:: DESCRIPTION

scHiCNorm is a software package for eliminating systematic biases in single-cell Hi-C data. Considering that single-cell Hi-C data are zero-inflated, here we use zero-inflated (Poisson and Negative Binomial) and hurdle (Poisson and Negative Binomial) models to remove biases, including cutting sites, GC content, and mappability.

::DEVELOPER

Z. WANG LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

scHiCNorm

:: MORE INFORMATION

Citation

Liu T, Wang Z.
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data.
Bioinformatics. 2018 Mar 15;34(6):1046-1047. doi: 10.1093/bioinformatics/btx747. PMID: 29186290; PMCID: PMC5860379.

HIPPO 1.5.0 – Heterogeneity Inspired pre-processing Tool

HIPPO 1.5.0

:: DESCRIPTION

HIPPO is a novel framework that leverages zero proportions to explain cellular heterogeneity and integrates feature selection with iterative clustering.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R 

:: DOWNLOAD

HIPPO

:: MORE INFORMATION

Citation

Kim TH, Zhou X, Chen M.
Demystifying “drop-outs” in single-cell UMI data.
Genome Biol. 2020 Aug 6;21(1):196. doi: 10.1186/s13059-020-02096-y. PMID: 32762710; PMCID: PMC7412673.

FlowAnd 1.0 – Analyze Largescale, Multi-color Flow Cytometry data

FlowAnd 1.0

:: DESCRIPTION

FlowAnd is designed to analyze and integrate largescale, multi-color flow cytometry data. It implements methods for data importing, various transformations, several clustering algorithms for automatic clustering, visualization tools as well as straightforward statistical testing.

::DEVELOPER

Hautaniemi Lab

:: SCREENSHOTS

FlowAnd

:: REQUIREMENTS

:: DOWNLOAD

 FlowAnd

:: MORE INFORMATION

Citation

Lahesmaa-Korpinen AM, Jalkanen SE, Chen P, Valo E, Nú?ez- Fontarnau J, et al. (2011)
FlowAnd: Comprehensive Computational Framework for Flow Cytometry Data Analysis
J Proteomics Bioinform 4: 245-249. doi:10.4172/ jpb.1000197

flowVS 1.24.0 – Variance Stabilization in Flow Cytometry

flowVS 1.24.0

:: DESCRIPTION

flowVS is a variance-stabilization algorithm that removes the mean-variance correlations from cell populations identified in each fluorescence channel.

::DEVELOPER

Ariful Azad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioConductor

:: DOWNLOAD

 flowVS

:: MORE INFORMATION

Citation

flowVS: channel-specific variance stabilization in flow cytometry.
Azad A, Rajwa B, Pothen A.
BMC Bioinformatics. 2016 Jul 28;17:291. doi: 10.1186/s12859-016-1083-9.