scHiCluster v0.1.1 – Single-cell Clustering algorithm for Hi-C Contact Matrices

scHiCluster v0.1.1

:: DESCRIPTION

scHiCluster is a comprehensive python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells.

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

scHiCluster

:: MORE INFORMATION

Citation:

Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR.
Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation.
Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14011-14018. doi: 10.1073/pnas.1901423116. Epub 2019 Jun 24. PMID: 31235599; PMCID: PMC6628819.

SCRIP 1.0.0 – An Accurate Simulator for Single-Cell RNA Sequencing Data

SCRIP 1.0.0

:: DESCRIPTION

SCRIP provides a flexible Gamma-Poisson mixture and a Beta-Gamma-Poisson mixture framework to simulate scRNA-seq data.

::DEVELOPER

Fei Qin [aut, cre, cph]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R

:: DOWNLOAD

SCRIP

:: MORE INFORMATION

Citation:

Qin F, Luo X, Xiao F, Cai G.
SCRIP: an accurate simulator for single-cell RNA sequencing data.
Bioinformatics. 2021 Dec 7:btab824. doi: 10.1093/bioinformatics/btab824. Epub ahead of print. PMID: 34874992.

RNA-Scoop v1.0.1 – Interactive Visualization of Single-cell Transcriptomes

RNA-Scoop v1.0.1

:: DESCRIPTION

RNA Scoop is a tool to visualize isoforms in single cell transcriptomes. Through use of an interactive cell cluster plot, users are able to explore isoforms in a single-cell transcriptome dataset of thousands of cells.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
JRE

:: DOWNLOAD

RNA Scoop

:: MORE INFORMATION

Citation

Stephenson M, Nip KM, HafezQorani S, Gagalova KK, Yang C, Warren RL, Birol I.
RNA-Scoop: interactive visualization of transcripts in single-cell transcriptomes.
NAR Genom Bioinform. 2021 Nov 29;3(4):lqab105. doi: 10.1093/nargab/lqab105. PMID: 34859209; PMCID: PMC8633890.

Scirpy v0.10.1 – Scanpy Extension for analyzing Single-cell T-cell Receptor-sequencing data

Scirpy v0.10.1

:: DESCRIPTION

Scirpy is a scalable python-toolkit to analyse T cell receptor (TCR) or B cell receptor (BCR) repertoires from single-cell RNA sequencing (scRNA-seq) data. It seamlessly integrates with the popular scanpy library and provides various modules for data import, analysis and visualization.

::DEVELOPER

the Institute of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

Scirpy

:: MORE INFORMATION

Citation

Sturm G, Szabo T, Fotakis G, Haider M, Rieder D, Trajanoski Z, Finotello F.
Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data.
Bioinformatics. 2020 Sep 15;36(18):4817-4818. doi: 10.1093/bioinformatics/btaa611. PMID: 32614448; PMCID: PMC7751015.

SCYN – Single Cell CNV profiling method using Dynamic Programming

SCYN

:: DESCRIPTION

SCYN is a CNV (Copy number variation) segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on in silico dataset.

::DEVELOPER

SCYN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

SCYN

:: MORE INFORMATION

Citation

Feng X, Chen L, Qing Y, Li R, Li C, Li SC.
SCYN: single cell CNV profiling method using dynamic programming.
BMC Genomics. 2021 Nov 16;22(Suppl 5):651. doi: 10.1186/s12864-021-07941-3. PMID: 34789142.

SIMBA v1.1 – SIngle-cell eMBedding Along with features

SIMBA v1.1

:: DESCRIPTION

SIMBA is a method to embed cells along with their defining features such as gene expression, transcription factor binding sequences and chromatin accessibility peaks into the same latent space.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Linux
R

:: DOWNLOAD

SIMBA

:: MORE INFORMATION

Citation

Preprint: Huidong Chen, Jayoung Ryu, Michael E. Vinyard, Adam Lerer & Luca Pinello.
“SIMBA: SIngle-cell eMBedding Along with features. bioRxiv, 2021.10.17.464750v1 (2021).”

singlecellVR – Interactive Visualization of Single-Cell Data in Virtual Reality

singlecellVR

:: DESCRIPTION

singlecellVR is a browser-contained, free, and open-access tool that allows users to interactively explore published studies or new data through an innovative VR interface. singlecellVR supports clustering, trajectory inference and abstract graph analysis for transcriptomic as well as epigenomic single cell data.

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

:: REQUIREMENTS

virtual reality hardware

:: DOWNLOAD

singlecellVR

:: MORE INFORMATION

Citation

Stein DF, Chen H, Vinyard ME, Qin Q, Combs RD, Zhang Q, Pinello L.
singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality.
Front Genet. 2021 Oct 28;12:764170. doi: 10.3389/fgene.2021.764170. PMID: 34777482; PMCID: PMC8582280.

STREAM v1.0 – Trajectory analysis from Single-cell RNAseq and ATACseq data

STREAM v1.0

:: DESCRIPTION

STREAM (Single-cell Trajectories Reconstruction, Exploration And Mapping) is an interactive computational pipeline for reconstructing complex celluar developmental trajectories from sc-qPCR, scRNA-seq or scATAC-seq data

::DEVELOPER

Pinello Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
Python

:: DOWNLOAD

STREAM

:: MORE INFORMATION

Citation

Nat Commun, 10 (1), 1903 2019 Apr 23
Single-cell Trajectories Reconstruction, Exploration and Mapping of Omics Data With STREAM
Huidong Chen, et al.

SCIP 1.0 – Single-Cell Image Processor

SCIP 1.0

:: DESCRIPTION

SCIP is an open source multi-channel, multi-process, time-lapse morphological and functional microscopy images analyser.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux/ MacOsX
MatLab

:: DOWNLOAD

SCIP

:: MORE INFORMATION

Citation:

Martins L, Neeli-Venkata R, Oliveira SMD, Häkkinen A, Ribeiro AS, Fonseca JM.
SCIP: a single-cell image processor toolbox.
Bioinformatics. 2018 Dec 15;34(24):4318-4320. doi: 10.1093/bioinformatics/bty505. PMID: 29931314.

WASP v1.0 – Web-Accessible Single Cell RNA-Seq Processing Platform

WASP v1.0

:: DESCRIPTION

WASP is a software covering the full range of analysis steps of a typical single-cell RNA sequencing workflow for Drop-Seq-based scRNA-Seq data.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows / MacOS
R
Python

:: DOWNLOAD

WASP

:: MORE INFORMATION

Citation

Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A.
WASP: a versatile, web-accessible single cell RNA-Seq processing platform.
BMC Genomics. 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6. PMID: 33736596; PMCID: PMC7977290.