Cargando…

dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments

Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troub...

Descripción completa

Detalles Bibliográficos
Autores principales:	Petukhov, Viktor, Guo, Jimin, Baryawno, Ninib, Severe, Nicolas, Scadden, David T., Samsonova, Maria G., Kharchenko, Peter V.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2018
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010209/ https://www.ncbi.nlm.nih.gov/pubmed/29921301 http://dx.doi.org/10.1186/s13059-018-1449-6

Ejemplares similares

RainDrop: Rapid activation matrix computation for droplet-based single-cell RNA-seq reads
por: Niebler, Stefan, et al.
Publicado: (2020)

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

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

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

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species
por: Tang, Jifeng, et al.
Publicado: (2006)

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

EST2Prot: Mapping EST sequences to proteins
por: Shafer, Paul, et al.
Publicado: (2006)

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

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

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

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

An ensemble approach to accurately detect somatic mutations using SomaticSeq
por: Fang, Li Tai, et al.
Publicado: (2015)

Magic-BLAST, an accurate RNA-seq aligner for long and short reads
por: Boratyn, Grzegorz M., et al.
Publicado: (2019)

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

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

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

galaxieEST: addressing EST identity through automated phylogenetic analysis
por: Nilsson, R Henrik, et al.
Publicado: (2004)

ContextMap 2: fast and accurate context-based RNA-seq mapping
por: Bonfert, Thomas, et al.
Publicado: (2015)

HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data
por: Yan, Huihuang, et al.
Publicado: (2014)

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

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
por: Choi, Ji-Hye, et al.
Publicado: (2020)

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)

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

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
por: Fan, Jeremy, et al.
Publicado: (2021)

SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning
por: Balaji, Advait, et al.
Publicado: (2022)

Fast-GBS: a new pipeline for the efficient and highly accurate calling of SNPs from genotyping-by-sequencing data
por: Torkamaneh, Davoud, et al.
Publicado: (2017)

EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries
por: Smith, Robin P, et al.
Publicado: (2008)

TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data
por: Clark, Lindsay V., et al.
Publicado: (2016)

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
por: Li, Bo, et al.
Publicado: (2011)

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)

PAVE: Program for assembling and viewing ESTs
por: Soderlund, Carol, et al.
Publicado: (2009)

Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq
por: Freeman, Trevor F., et al.
Publicado: (2023)

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
por: Testa, Alison C, et al.
Publicado: (2015)

Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design
por: Field, Helen I, et al.
Publicado: (2009)

SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models
por: Reid, Ian, et al.
Publicado: (2014)

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration
por: Forment, Javier, et al.
Publicado: (2008)

Bioinformatic pipelines in Python with Leaf
por: Napolitano, Francesco, et al.
Publicado: (2013)

Tools and pipelines for BioNano data: molecule assembly pipeline and FASTA super scaffolding tool
por: Shelton, Jennifer M., et al.
Publicado: (2015)

QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing
por: Zhao, Shanrong, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_qclj2p7sf0babcvj148e92rgbo