Tag: Single Cell

SCAN-SNV – Single Cell Somatic Genotyper

SCAN-SNV

:: DESCRIPTION

SCAN-SNV (Single Cell ANalysis of SNVs) identifies somatic single nucleotide variants (sSNVs) from whole genome amplified single cell DNA-seq.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

SCAN-SNV

:: MORE INFORMATION

Citation

Luquette LJ, Bohrson CL, Sherman MA, Park PJ.
Identification of somatic mutations in single cell DNA-seq using a spatial model of allelic imbalance.
Nat Commun. 2019 Aug 29;10(1):3908. doi: 10.1038/s41467-019-11857-8. PMID: 31467286; PMCID: PMC6715686.

scRNABatchQC v0.10.3 – multi-samples Quality Control for single cell RNA-seq data

scRNABatchQC v0.10.3

:: DESCRIPTION

scRNABatchQC is an R package for generating a HTML QC report to check and compare quality of multiple single cell RNA-seq datasets. scRNABatchQC supports multiple types of inputs, including gene-cell count matrices, 10x genomics, SingleCellExperiment or Seurat v3 objects.

::DEVELOPER

scRNABatchQC team

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

scRNABatchQC

:: MORE INFORMATION

Citation

Liu Q, Sheng Q, Ping J, Ramirez MA, Lau KS, Coffey RJ, Shyr Y.
scRNABatchQC: multi-samples quality control for single cell RNA-seq data.
Bioinformatics. 2019 Dec 15;35(24):5306-5308. doi: 10.1093/bioinformatics/btz601. PMID: 31373345; PMCID: PMC6954654.

netSmooth v0.1.0 – A Network smoothing based method for single cell RNA-seq

netSmooth v0.1.0

:: DESCRIPTION

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using gene interaction networks such as protein- protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNA-seq data.

::DEVELOPER

Bioinformatics & Omics Data Science platform

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

netSmooth

:: MORE INFORMATION

Citation

Ronen J, Akalin A.
netSmooth: Network-smoothing based imputation for single cell RNA-seq.
F1000Res. 2018 Jan 3;7:8. doi: 10.12688/f1000research.13511.3. PMID: 29511531; PMCID: PMC5814748.

novoSpaRc 0.4.3 – de novo Spatial Reconstruction of Single-Cell Gene Expression

novoSpaRc 0.4.3

:: DESCRIPTION

novoSpaRc predicts locations of single cells in space by solely using single-cell RNA sequencing data.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

novoSpaRc

:: MORE INFORMATION

Citation

Moriel N, Senel E, Friedman N, Rajewsky N, Karaiskos N, Nitzan M.
NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Nat Protoc. 2021 Sep;16(9):4177-4200. doi: 10.1038/s41596-021-00573-7. Epub 2021 Aug 4. PMID: 34349282.

SPAdes 3.15.3 – Single-cell Genome Assembler

SPAdes 3.15.3

:: DESCRIPTION

SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.

::DEVELOPER

Center for Algorithmic Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

 SPAdes

:: MORE INFORMATION

Citation

Nurk S, Meleshko D, Korobeynikov A, Pevzner PA.
metaSPAdes: a new versatile metagenomic assembler.
Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15. PMID: 28298430; PMCID: PMC5411777.

hybridSPAdes: an algorithm for hybrid assembly of short and long reads.
Antipov D, Korobeynikov A, McLean JS, Pevzner PA.
Bioinformatics. 2015 Nov 20. pii: btv688

Anton Bankevich,et al.
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.
Journal of Computational Biology 19(5) (2012), 455-477. doi:10.1089/cmb.2012.0021

ISOP 0.99.1 – Isoform-level expression patterns in single-cell RNA-sequencing data

ISOP 0.99.1

:: DESCRIPTION

ISOP (ISOform Patterns) is a mixture model o characterize the expression patterns of pairs of isoform from the same genes and determine if isoform-level expression patterns are random or signify biological effects.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

ISOP

:: MORE INFORMATION

Citation

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Pawitan Y, Rantalainen M.
Isoform-level gene expression patterns in single-cell RNA-sequencing data.
Bioinformatics. 2018 Jul 15;34(14):2392-2400. doi: 10.1093/bioinformatics/bty100. PMID: 29490015; PMCID: PMC6041805.

BPSC v0.99.2 – Beta-Poisson model for single-cell RNA-seq data analyses

BPSC v0.99.2

:: DESCRIPTION

BPSC is a beta-Poisson mixture model that can capture the bimodality of the single-cell gene expression distribution. The BPSC model is into the generalized linear model (GLM) framework in order to perform differential expression analyses.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

BPSC

:: MORE INFORMATION

Citation

Vu TN, Wills QF, Kalari KR, Niu N, Wang L, Rantalainen M, Pawitan Y.
Beta-Poisson model for single-cell RNA-seq data analyses.
Bioinformatics. 2016 Jul 15;32(14):2128-35. doi: 10.1093/bioinformatics/btw202. Epub 2016 Apr 19. PMID: 27153638.

SCmut – Detect Cell-level Mutation from single-cell RNA-sequencing

SCmut

:: DESCRIPTION

SCmut is a novel and robust statistical method for cell-level somatic mutation detection from single-cell RNA-sequencing.

::DEVELOPER

PROF. YUDI PAWITAN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

SCmut

:: MORE INFORMATION

Citation

Vu TN, Nguyen HN, Calza S, Kalari KR, Wang L, Pawitan Y.
Cell-level somatic mutation detection from single-cell RNA sequencing.
Bioinformatics. 2019 Nov 1;35(22):4679-4687. doi: 10.1093/bioinformatics/btz288. PMID: 31028395; PMCID: PMC6853710.

Velvet-SC 0.7.62 – Velvet modified for Single Cell reads

Velvet-SC 0.7.62

:: DESCRIPTION

Velvet-SC is a Velvet modified software for Single Cell reads

::DEVELOPER

UCSD Department of Computer Science and Engineering

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Velvet-SC

:: MORE INFORMATION

Citation

Hamidreza Chitsaz, Joyclyn L. Yee-Greenbaum, Glenn Tesler, Mary-Jane Lombardo, Christopher L. Dupont, Jonathan H. Badger, Mark Novotny, Douglas B. Rusch, Louise J. Fraser, Niall A. Gormley, Ole Schulz-Trieglaff, Geoffrey P. Smith, Dirk J. Evers, Pavel A. Pevzner, Roger S. Lasken.
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Nature Biotechnology, vol. 29, no. 11, pp. 915-921 (2011), advance online publication, 18 Sep 2011

BAIT 1.4 – Organizing Genomes and Mapping Rearrangements in Single Cells

BAIT 1.4

:: DESCRIPTION

BAIT (Bioinformatic Analysis of Inherited Templates) is a software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

::DEVELOPER

Terry Fox Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • SAMtools
  • BEDtools
  • R
  • DNAcopy R package
  • gplots R package.

:: DOWNLOAD

 BAIT

:: MORE INFORMATION

Citation

Genome Med. 2013 Sep 13;5(9):82.
BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M1, O’Neill K, Falconer E, Brinkman R, Lansdorp PM.