Cargando…

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

BACKGROUND: Recent advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the identification of individual cell types, such as epithelial cells, immune cells, and fibroblasts, in tissue samples containing complex cell populations. Cell typing is one of the key challenges in scRNA...

Descripción completa

Detalles Bibliográficos
Autores principales:	Choi, Ji-Hye, In Kim, Hye, Woo, Hyun Goo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2020
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430822/ https://www.ncbi.nlm.nih.gov/pubmed/32753029 http://dx.doi.org/10.1186/s12859-020-03700-5

Ejemplares similares

scDIOR: single cell RNA-seq data IO software
por: Feng, Huijian, et al.
Publicado: (2022)

SEQprocess: a modularized and customizable pipeline framework for NGS processing in R package
por: Joo, Taewoon, et al.
Publicado: (2019)

Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists
por: Zhu, Xun, et al.
Publicado: (2017)

scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing
por: Li, Kejie, et al.
Publicado: (2023)

scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis
por: Wong, John K. L., et al.
Publicado: (2023)

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments
por: Petukhov, Viktor, et al.
Publicado: (2018)

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
por: Qin, Qian, et al.
Publicado: (2016)

ARPIR: automatic RNA-Seq pipelines with interactive report
por: Spinozzi, Giulio, et al.
Publicado: (2020)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
por: Cornwell, MacIntosh, et al.
Publicado: (2018)

IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods
por: Yan, Aimin, et al.
Publicado: (2023)

Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites
por: Furstenau, Tara N., et al.
Publicado: (2018)

scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data
por: Yu, Wenbao, et al.
Publicado: (2020)

Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline
por: Smith, David Roy, et al.
Publicado: (2017)

Fully automated pipeline for detection of sex linked genes using RNA-Seq data
por: Michalovova, Monika, et al.
Publicado: (2015)

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
por: Audoux, Jérôme, et al.
Publicado: (2017)

An interpretable framework for clustering single-cell RNA-Seq datasets
por: Zhang, Jesse M., et al.
Publicado: (2018)

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
por: Ather, Syed Hussain, et al.
Publicado: (2020)

NetSeekR: a network analysis pipeline for RNA-Seq time series data
por: Srivastava, Himangi, et al.
Publicado: (2022)

scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
por: Nguyen, Vy, et al.
Publicado: (2022)

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data
por: Hu, Kai, et al.
Publicado: (2022)

TAP: a targeted clinical genomics pipeline for detecting transcript variants using RNA-seq data
por: Chiu, Readman, et al.
Publicado: (2018)

Automated Isoform Diversity Detector (AIDD): a pipeline for investigating transcriptome diversity of RNA-seq data
por: Plonski, Noel-Marie, et al.
Publicado: (2020)

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
por: Eagles, Nicholas J., et al.
Publicado: (2021)

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data
por: Romagnoli, Dario, et al.
Publicado: (2018)

Identification of cell barcodes from long-read single-cell RNA-seq with BLAZE
por: You, Yupei, et al.
Publicado: (2023)

iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq
por: Giurato, Giorgio, et al.
Publicado: (2013)

RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data
por: Zhou, Qian, et al.
Publicado: (2018)

scSTEM: clustering pseudotime ordered single-cell data
por: Song, Qi, et al.
Publicado: (2022)

Single Cell Explorer, collaboration-driven tools to leverage large-scale single cell RNA-seq data
por: Feng, Di, et al.
Publicado: (2019)

scQCEA: a framework for annotation and quality control report of single-cell RNA-sequencing data
por: Nassiri, Isar, et al.
Publicado: (2023)

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data
por: Sun, Zhifu, et al.
Publicado: (2014)

scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor
por: Amarasinghe, Shanika L, et al.
Publicado: (2023)

SC3s: efficient scaling of single cell consensus clustering to millions of cells
por: Quah, Fu Xiang, et al.
Publicado: (2022)

CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data
por: Lin, Peijie, et al.
Publicado: (2017)

NDRindex: a method for the quality assessment of single-cell RNA-Seq preprocessing data
por: Xiao, Ruiyu, et al.
Publicado: (2020)

WASP: a versatile, web-accessible single cell RNA-Seq processing platform
por: Hoek, Andreas, et al.
Publicado: (2021)

Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data
por: Kurtenbach, Stefan, et al.
Publicado: (2021)

scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
por: Bertolini, Anne, et al.
Publicado: (2022)

FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data
por: DeTomaso, David, et al.
Publicado: (2016)

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
por: Falgueras, Juan, et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_neodgps02shqncn7jbpv9qkfm6