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  • SPAdes
  • Referenced in 12 articles [sw17004]
  • goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome ... assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly ... SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that ... cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single...

  • MAST
  • Referenced in 5 articles [sw30709]
  • heterogeneity in single-cell RNA sequencing data. Single-cell transcriptomics reveals gene expression heterogeneity ... part, generalized linear model for such bimodal data that parameterizes both of these features ... fraction of genes expressed in a cell, should be adjusted for as a source ... gene set enrichment analysis tailored to single-cell data. It provides insights into how networks...

  • ZIFA
  • Referenced in 7 articles [sw32141]
  • single-cell gene expression analysis. Single-cell RNA-seq data allows insight into normal cellular ... single cell level. Dimensionality reduction of such high-dimensional data sets is essential ... visualization and analysis, but single-cell RNA-seq data are challenging for classical dimensionality-reduction...

  • SC3
  • Referenced in 3 articles [sw23914]
  • clustering of single-cell RNA-seq data. Single-cell RNA-seq enables the quantitative characterization...

  • CIDR
  • Referenced in 4 articles [sw32140]
  • accurate clustering through imputation for single-cell RNA-seq data. Most existing dimensionality reduction ... clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy...

  • MEMO
  • Referenced in 1 article [sw34231]
  • simultaneous, automated analysis of censored and uncensored data acquired under multiple experimental conditions. MEMO ... applied to a variety of different single-cell data types. We demonstrate the advantages ... analyzing right and interval censored single-cell microscopy data. Our results show that an examination ... allows for a stringent analysis of single-cell data and enables researchers to avoid misinterpretation...

  • SPRING
  • Referenced in 1 article [sw34137]
  • interface for visualizing high dimensional single-cell expression data. Motivation: Single-cell gene expression profiling ... need for computational tools to explore the data they produce. In particular, visualizing continuous gene...

  • SCENIC
  • Referenced in 1 article [sw29313]
  • cell-state identification from single-cell RNA-seq data ... scenic.aertslab.org). On a compendium of single-cell data from tumors and brain, we demonstrate that...

  • SPhyR
  • Referenced in 1 article [sw34136]
  • SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. Results ... tumor phylogeny estimation from single-cell sequencing data. In light of frequent loss of SNVs...

  • cisTopic
  • Referenced in 1 article [sw35766]
  • Regulatory topic modelling on single-cell ATAC-seq data. We present cisTopic, a probabilistic framework ... stable cell states from sparse single-cell epigenomics data (http://github.com/aertslab/cistopic). On a compendium...

  • SEQuel
  • Referenced in 2 articles [sw16992]
  • While assemblies of next generation sequencing (NGS) data are accurate, they still contain a substantial ... both standard (multi-cell) and single-cell sequencing data. SEQuel was tested mainly on Illumina...

  • splatter
  • Referenced in 1 article [sw33834]
  • Bioconductor/R package Simple Simulation of Single-cell RNA Sequencing Data. Splatter is a package ... simulation of single-cell RNA sequencing count data. It provides a simple interface for creating...

  • scran
  • Referenced in 1 article [sw19472]
  • package scran. Methods for Single-Cell RNA-Seq Data Analysis. Implements a variety ... level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell...

  • clusterExperiment
  • Referenced in 1 article [sw36155]
  • comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data...

  • slingshot
  • Referenced in 1 article [sw36159]
  • single-cell sequencing. Provides functions for inferring continuous, branching lineage structures in low-dimensional data ... model developmental trajectories in single-cell RNA sequencing data and serve as a component...

  • zinbwave

  • Referenced in 2 articles [sw36151]
  • Inflated Negative Binomial Model for RNA-Seq Data. Implements a general and flexible zero-inflated ... dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts...

  • TRONCO
  • Referenced in 1 article [sw19759]
  • cancer progression models from heterogeneous genomic data. Motivation: We introduce TRONCO (TRanslational ONCOlogy), an open ... samples, e.g., multiple biopsies or single-cell sequencing data, are available. The resulting models...

  • powsimR
  • Referenced in 1 article [sw34191]
  • powsimR: power analysis for bulk and single cell RNA-seq experiments. Summary: Power analysis ... detect differentially expressed genes in RNA-seq data. PowsimR is a flexible tool to simulate ... expression from bulk and especially single-cell RNA-seq data making it suitable...

  • AgentCell
  • Referenced in 6 articles [sw35544]
  • develop new computational approaches at the single-cell level. Results: We have developed AgentCell ... stochastic intracellular processes and behavior of individual cells. As a test-bed for our approach ... cells are free to move in a 3D environment. Digital chemotaxis assays reproduce experimental data...