Orchestrating high-throughput genomic analysis with Bioconductor
Bioconductor is an open-source, open-development software project for the analysis and
comprehension of high-throughput data in genomics and molecular biology. The project …
comprehension of high-throughput data in genomics and molecular biology. The project …
Orchestrating single-cell analysis with Bioconductor
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …
genome-wide features in individual cells. However, single-cell data present unique …
Software for computing and annotating genomic ranges
M Lawrence, W Huber, H Pagès… - PLoS computational …, 2013 - journals.plos.org
We describe Bioconductor infrastructure for representing and computing on annotated
genomic ranges and integrating genomic data with the statistical computing features of R …
genomic ranges and integrating genomic data with the statistical computing features of R …
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Abstract Background Chromatin immunoprecipitation (ChIP) followed by high-throughput
sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have …
sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have …
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data
M Morgan, S Anders, M Lawrence, P Aboyoun… - …, 2009 - academic.oup.com
ShortRead is a package for input, quality assessment, manipulation and output of high-
throughput sequencing data. ShortRead is provided in the R and Bioconductor …
throughput sequencing data. ShortRead is provided in the R and Bioconductor …
Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin
In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the
nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and …
nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and …
Relational drivers of the agroecological transition: An analysis of farmer trajectories in the Limagne plain, France
E Polge, H Pagès - Agricultural Systems, 2022 - Elsevier
CONTEXT The social network analysis of farmers who have adopted agroecological
practices give the possibility to identify which actors are involved in the agroecological …
practices give the possibility to identify which actors are involved in the agroecological …
Genomic annotation resources in R/Bioconductor
MRJ Carlson, H Pagès, S Arora, V Obenchain… - … Genomics: Methods and …, 2016 - Springer
Annotation resources make up a significant proportion of the Bioconductor project (Huber et
al., Nat Methods 12: 115–121, 2015). And there are also a diverse set of online resources …
al., Nat Methods 12: 115–121, 2015). And there are also a diverse set of online resources …
[HTML][HTML] Orchestrating spatial transcriptomics analysis with bioconductor
Spatial transcriptomics technologies provide spatially-resolved measurements of gene
expression through assays that can either target selected genes or capture transcriptome …
expression through assays that can either target selected genes or capture transcriptome …
[PDF][PDF] Package 'annotationdbi'
H Pagès, M Carlson, S Falcon… - Bioconductor …, 2017 - bioconductor.statistik.tu-dortmund.de
Collate 00RTobjs. R AllGenerics. R AllClasses. R unlist2. R utils. R SQL. R FlatBimap. R
AnnDbObj-lowAPI. R Bimap. R GOTerms. R BimapFormatting. R Bimap-envirAPI. R flatten …
AnnDbObj-lowAPI. R Bimap. R GOTerms. R BimapFormatting. R Bimap-envirAPI. R flatten …