Cargando…

Semla: a versatile toolkit for spatially resolved transcriptomics analysis and visualization

SUMMARY: Spatially resolved transcriptomics technologies generate gene expression data with retained positional information from a tissue section, often accompanied by a corresponding histological image. Computational tools should make it effortless to incorporate spatial information into data analy...

Descripción completa

Detalles Bibliográficos
Autores principales:	Larsson, Ludvig, Franzén, Lovisa, Ståhl, Patrik L, Lundeberg, Joakim
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Applications Note
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10597621/ https://www.ncbi.nlm.nih.gov/pubmed/37846051 http://dx.doi.org/10.1093/bioinformatics/btad626

Ejemplares similares

GeneticsMakie.jl: a versatile and scalable toolkit for visualizing locus-level genetic and genomic data
por: Kim, Minsoo, et al.
Publicado: (2022)

KAnalyze: a fast versatile pipelined K-mer toolkit
por: Audano, Peter, et al.
Publicado: (2014)

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor
por: Righelli, Dario, et al.
Publicado: (2022)

Seamless integration of image and molecular analysis for spatial transcriptomics workflows
por: Bergenstråhle, Joseph, et al.
Publicado: (2020)

Jutils: a visualization toolkit for differential alternative splicing events
por: Yang, Guangyu, et al.
Publicado: (2021)

VISTA: visualizing the spatial transcriptome of the C.elegans nervous system
por: Liska, David, et al.
Publicado: (2023)

Unravelling spatial gene associations with SEAGAL: a Python package for spatial transcriptomics data analysis and visualization
por: Wang, Linhua, et al.
Publicado: (2023)

HATK: HLA analysis toolkit
por: Choi, Wanson, et al.
Publicado: (2020)

ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data
por: Huang, Xiaosan, et al.
Publicado: (2018)

Comprehensive visualization of cell–cell interactions in single-cell and spatial transcriptomics with NICHES
por: Raredon, Micha Sam Brickman, et al.
Publicado: (2022)

CGAT: computational genomics analysis toolkit
por: Sims, David, et al.
Publicado: (2014)

CRAVAT: cancer-related analysis of variants toolkit
por: Douville, Christopher, et al.
Publicado: (2013)

Haptools: a toolkit for admixture and haplotype analysis
por: Massarat, Arya R, et al.
Publicado: (2023)

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
por: Bergenstråhle, Joseph, et al.
Publicado: (2020)

Social Media Mining Toolkit (SMMT)
por: Tekumalla, Ramya, et al.
Publicado: (2020)

Destin: toolkit for single-cell analysis of chromatin accessibility
por: Urrutia, Eugene, et al.
Publicado: (2019)

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues
por: Berglund, Emelie, et al.
Publicado: (2020)

MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor
por: Peters Couto, Bárbara Zita, et al.
Publicado: (2023)

WIST: toolkit for rapid, customized LIMS development
por: Huang, Y. Wayne, et al.
Publicado: (2011)

The Bio-Community Perl toolkit for microbial ecology
por: Angly, Florent E., et al.
Publicado: (2014)

CART—a chemical annotation retrieval toolkit
por: Deghou, Samy, et al.
Publicado: (2016)

Single-Cell Virtual Cytometer allows user-friendly and versatile analysis and visualization of multimodal single cell RNAseq datasets
por: Pont, Frédéric, et al.
Publicado: (2020)

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries
por: Barquist, Lars, et al.
Publicado: (2016)

DEP2: an upgraded comprehensive analysis toolkit for quantitative proteomics data
por: Feng, Zhenhuan, et al.
Publicado: (2023)

Poretools: a toolkit for analyzing nanopore sequence data
por: Loman, Nicholas J., et al.
Publicado: (2014)

BamToCov: an efficient toolkit for sequence coverage calculations
por: Birolo, Giovanni, et al.
Publicado: (2022)

iSC.MEB: an R package for multi-sample spatial clustering analysis of spatial transcriptomics data
por: Zhang, Xiao, et al.
Publicado: (2023)

CATMAID: collaborative annotation toolkit for massive amounts of image data
por: Saalfeld, Stephan, et al.
Publicado: (2009)

SNPTransformer: A Lightweight Toolkit for Genome-Wide Association Studies
por: Dong, Changzheng
Publicado: (2010)

SquiggleKit: a toolkit for manipulating nanopore signal data
por: Ferguson, James M, et al.
Publicado: (2019)

Swan: a library for the analysis and visualization of long-read transcriptomes
por: Reese, Fairlie, et al.
Publicado: (2020)

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
por: Chaumeil, Pierre-Alain, et al.
Publicado: (2020)

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows
por: Lemoine, Frédéric, et al.
Publicado: (2021)

CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
por: Przytycki, Pawel F, et al.
Publicado: (2022)

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
por: Mapleson, Daniel, et al.
Publicado: (2017)

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer
por: Wong, Wing Chung, et al.
Publicado: (2011)

Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit
por: Dijkstra, Maurits J J, et al.
Publicado: (2019)

LRez: a C++ API and toolkit for analyzing and managing Linked-Reads data
por: Morisse, Pierre, et al.
Publicado: (2021)

cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly
por: Lewis, T E, et al.
Publicado: (2019)

Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples
por: Mirzazadeh, Reza, et al.
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_e6t88kle4s8q1hmsrpugfaiq03