Category: Cytometry / Cell

CIRCLET – Circular Trajectory Reconstruction tool

CIRCLET

:: DESCRIPTION

CIRCLET is a powerful and robust circular trajectory reconstruction tool without specifying a starting cell for resolving cell cycle phases of single cells by considering multi-scale features of chromosomal architectures. CIRCLET reveals its best superiority based on the combination of a feature set about global information and two feature sets about local interactional information in terms of designed evaluation indexes and verification strategies from a collection of cell cycle Hi-C maps.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Python

:: DOWNLOAD

CIRCLET

:: MORE INFORMATION

Citation

Ye Y, Gao L, Zhang S.
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps.
Adv Sci (Weinh). 2019 Sep 30;6(23):1900986. doi: 10.1002/advs.201900986. PMID: 31832309; PMCID: PMC6891923.

JRIM – Joint reconstruct cis-regulatory interaction networks of multiple cell populations

JRIM

:: DESCRIPTION

JRIM is a package for Jointly Reconstructing cis-regulatory Interaction Maps of multiple cell populations using single-cell chromatin accessibility data and identifying shared and common interaction patterns. It uses an aggregation process to deal with the sparsity of single-cell data, exploits similarity between cell types via a group lasso penalty, and generates comparable networks. JRIM could be used to characterize difference between cell types or identify dynamic changes during cell development.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • R

:: DOWNLOAD

JRIM

:: MORE INFORMATION

Citation

Dong K, Zhang S.
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data.
Brief Bioinform. 2021 May 20;22(3):bbaa120. doi: 10.1093/bib/bbaa120. PMID: 32578841; PMCID: PMC8138825.

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.

THANATOS 1.0 – THe Apoptosis, Necrosis, AUtophagy OrchestratorS

THANATOS 1.0

:: DESCRIPTION

The THANATOS (Apoptosis, Necrosis and Autophagy) database is the first integrative resource to pin point most of identified components and related scientific information of cell death (apoptosis, necrosis and/or autophagy).

::DEVELOPER

The CUCKOO Workgroup

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

Citation

THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy and cell death pathways.
Lili Ma, Zexian Liu, Ying Zhang, Yongbo Wang, Wankun Deng, Yaping Wei, Shahid Ullah, and Yu Xue.
Submitted

FlowJo v10.7 – Analysis Package for Flow Cytometrists

FlowJo v10.7

:: DESCRIPTION

FlowJo is like the Swiss army knife of Flow Cytometric analysis programs. FlowJo analyzes data collected by a flow cytometer (data from the cytometer must be saved as an fcs compliant file). FlowJo’s strength is in analyzing whole experiments encompassing many related samples. In addition to gating and statistics, FlowJo also can analyze DNA/Cell Cycle, Kinetics, and Proliferation Experiments. FlowJo has sophisticated tools for generating statistics, graphs, tables, webpages, and even movies.

::DEVELOPER

Tree Star, Inc.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FlowJo

:: MORE INFORMATION

QUALIFIER 1.26.1 – Qualitiy Control for Gated Flow Cytometry data

QUALIFIER 1.26.1

:: DESCRIPTION

The QUAliFiER package takes advantage of the manual gates to perform an extensive series of statistical quality assessment checks on the gated cell sub-populations while taking into account the structure of the data and the study design to monitor the consistency of population statistics across staining panels, subject, aliquots, channels, or other experimental variables.

::DEVELOPER

Raphael Gottardo’s Research Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX /Windows
  • R package
  • BioConductor

:: DOWNLOAD

 QUALIFIER

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Sep 28;13:252. doi: 10.1186/1471-2105-13-252.
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.
Finak G, Jiang W, Pardo J, Asare A, Gottardo R.

RchyOptimyx 2.32.0 – Optimyzed Cellular Hierarchies for Flow Cytometry

RchyOptimyx 2.32.0

:: DESCRIPTION

RchyOptimyx constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  RchyOptimyx

:: MORE INFORMATION

Citation

Cytometry A. 2012 Dec;81(12):1022-30. doi: 10.1002/cyto.a.22209. Epub 2012 Oct 8.
RchyOptimyx: cellular hierarchy optimization for flow cytometry.
Aghaeepour N1, Jalali A, O’Neill K, Chattopadhyay PK, Roederer M, Hoos HH, Brinkman RR.

flowCL 1.30.0 – Semantic labelling of Flow Cytometric Cell Populations

flowCL 1.30.0

:: DESCRIPTION

flowCL is a software package that performs semantic labelling of cell populations based on their surface markers and applied it to labelling of the Federation of Clinical Immunology Societies Human Immunology Project Consortium lyoplate populations as a use case.

::DEVELOPER

Justin Meskas <jmeskas at bccrc.ca>, Radina Droumeva

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • BioConductor

:: DOWNLOAD

 flowCL

:: MORE INFORMATION

Citation

flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Renani JT, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR.
Bioinformatics. 2014 Dec 6. pii: btu807.