| Title: | Human macrophage immune response |
|---|---|
| Description: | This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", published in Nature Genetics, January 2018. For details on version numbers and how the samples were processed see the package vignette. |
| Authors: | Michael Love |
| Maintainer: | Michael Love <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.29.1 |
| Built: | 2026-10-10 10:40:46 UTC |
| Source: | https://github.com/bioc/macrophage |
This package provides the output of running Salmon on a set of 24 RNA-seq samples from Alasoo, et al. (2018). For more details on the data and steps used to generate the quantification files, please refer to the package vignette.
Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
Estimated counts, abundance and effective length per gene for macrophage RNA-Seq experiment
data("gse")data("gse")
RangedSummarizedExperiment
This package provides the output of running Salmon on a set
of 24 RNA-seq samples from Alasoo, et al. (2018).
For more details on the data and steps used to generate the
quantification files, please refer to the package vignette.
For the script used to build the gse object, see the
gse_create.R script in the scripts directory.
FASTQ files from ENA
Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", Nature Genetics, January 2018 doi: 10.1038/s41588-018-0046-7.
A table mapping all transcripts of the Gencode v29 human reference
(as indexed by Salmon for the macrophage dataset) to genes. It can be
used to summarize macro_txp_se to the gene level with
tximeta::summarizeToGene(se, skipRanges=TRUE, tx2gene=macro_tx2gene),
which does not require the GTF file. For the script used to build this
object, see makeSumExp.R in the scripts directory of the
installed package.
data("macro_tx2gene")data("macro_tx2gene")
A DataFrame with 205870 rows and columns
tx_name and gene_id.
Gencode v29 human reference transcripts
Salmon quantification of 24 RNA-seq samples from Alasoo, et al. (2018),
imported with tximeta, including the 20 inferential replicates
from Salmon's Gibbs sampler (assays infRep1, ..., infRep20).
It is used in the swish vignette of the fishpond package.
data("macro_txp_se")data("macro_txp_se")
A RangedSummarizedExperiment with 15294 transcripts
and 24 samples. Assays: counts, abundance,
length, and infRep1, ..., infRep20.
colData columns: names, id, line,
condition.
To reduce size, the object contains all transcripts of a random subset
of 2000 expressed genes (at least one transcript with a count of 10 or
more in 3 or more samples) plus the GBP gene family (GBP1-GBP7), and the
counts and infRep assays are rounded to 1 decimal.
The full Salmon output for all transcripts, including the inferential
replicates, is archived on Zenodo:
doi:10.5281/zenodo.22982581.
For the script used to build this object, see makeSumExp.R
in the scripts directory of the installed package.
FASTQ files from ENA
Alasoo, et al. "Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response", Nature Genetics, January 2018 doi:10.1038/s41588-018-0046-7.