Package Usage : cran : SummarizedExperiment
Explore the latest package usage data for SummarizedExperiment in the cran ecosystem, including detailed information on package dependencies and their usage.
Total dependents: 543
Total downloads: 2,567,533
More details on packages.ecosyste.ms - JSON
veupathdb/rserve 8.2.2
- version: 1.28.0
ccdlstaging/dr_downloaders 1.45.8
- version: 1.8.1
broadinstitute/terra-jupyter-aou 2.1.13
- version: 1.28.0, 1.24.0
ccdlstaging/dr_affymetrix 1.45.8
- version: 1.8.1
nfcore/methylseq 1.6.1
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel.
- version: 1.22.0
ccdlstaging/dr_salmon 1.45.8
- version: 1.8.1
nfcore/atacseq 1.2.2
A Docker container for the nf-core/atacseq pipeline.
- version: 1.16.0
biocontainers/control-freec v11.5_cv1
- version: 1.0.2
nfcore/chipseq 1.2.2
A docker image for nf-core/chipseq
- version: 1.18.1
nfcore/eager 2.5.3
A Docker image for the nf-core/eager pipeline.
- version: 1.20.0
mirekphd/ml-cpu-r40-rs-cust 20230912
- version: 1.30.2
dhspence/docker-genomic-analysis 122121
From Chris Miller's example
- version: 1.16.1
mirekphd/ml-cpu-r36-rs-cust latest
- version: 1.8.0
ccdlstaging/dr_no_op 1.45.8
- version: 1.8.1
nfcore/ampliseq 1.2.0
A Docker image for nf-core/ampliseq.
- version: 1.12.0
mirekphd/ml-cpu-r36-base latest
- version: 1.8.0
biocontainers/isee-galaxy v3.13_cv1.0.0
- version: 1.23.1
ccdlstaging/dr_smasher 1.45.8
- version: 1.8.1
ccdlstaging/dr_illumina 1.45.8
- version: 1.8.1
patroonorg/patroondeps latest
- version: 1.28.0
dhspence/docker-biscuit latest
- version: 1.10.1
ccdlstaging/dr_compendia 1.45.8
- version: 1.8.1
nfcore/airrflowreport dev
- version: 1.28.0
nfcore/circrna dev
Workflow for analysis and miRNA target prediction analysis of circRNAs in RNA-Seq data.
- version: 1.16.0
nfcore/sarek 2.7.2
A Docker container for the nf-core/sarek pipeline
- version: 1.20.0
nfcore/slamseq 1.0.0
A docker image for nf-core/slamseq
- version: 1.12.0
nfcore/hic 1.3.0
A docker container for the nf-core/hic pipeline.
- version: 1.18.1
nfcore/nanoseq 1.1.0
Nanopore demultiplexing, QC and alignment pipeline
- version: 1.20.0
nfcore/scrnaseq 1.1.0
A Docker Container for the nf-core/scrnaseq pipeline.
- version: 1.16.0
mirekphd/ml-cpu-r35-rs 20190201
- version: 1.10.1
dhspence/docker-homer latest
docker with chip-seq tool homer
- version: 1.10.1
nfcore/exoseq dev
A docker container for the ExoSeq pipeline
- version: 1.10.1
nfcore/lncpipe dev
A Docker image for nf-core/lncpipe
- version: 1.10.1
seglh/exomedepth f4716ad
- version: 1.26.1
veitveit/vsclust release-1.3.2
For more details, see https://bitbucket.org/veitveit/vsclust
- version: 1.28.0
dhspence/docker-sicer latest
- version: 1.10.1
qdidiscoveryservices/limma-voom 4.2.0
- version: 1.26.1
qdidiscoveryservices/cellranger7.0.1_py3_r4 v1.2.2
- version: 1.24.0
dhspence/docker-basestation latest
- version: 1.10.1
qdidiscoveryservices/py3_cellranger 6.1.2
- version: 1.18.1
dhspence/docker-dss latest
- version: 1.16.1
biocontainers/bioconductor-cummerbund v2.16.0-2-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-bsgenome v1.42.0-2-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-variantannotation v1.20.2-1b1-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-ensembldb v1.6.2-1-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-shortread v1.32.0-1b1-deb_cv1
- version: 1.4.0
tercen/runtime-flowsuite 3.15-4
- version: 1.26.1
cimendes/splicing-pipelines-nf 3.1.ubuntu
- version: 1.22.0
biocontainers/bioconductor-genomicalignments v1.10.0-1b1-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-biovizbase v1.22.0-2-deb_cv1
- version: 1.4.0
koki/sctensor-experiments 20220208
- version: 1.24.0
evolbioinfo/deseq2 v1.28.1
- version: 1.18.2
qdidiscoveryservices/scrna_downstream 1.1
- version: 1.22.0
recetox/ramclustr 1.1.0-recetox0
- version: 1.18.2
koki/biocdev 20230818
- version: 1.31.1
anand7899/rmarkdown latest
- version: 1.28.0
prismcmap/sushi v0.0.2
- version: 1.20.0
hoonbiolab/hmftools v1.1
- version: 1.22.0
qdidiscoveryservices/bam_to_10x_counts latest
- version: 1.24.0
biocontainers/bioconductor-rtracklayer v1.34.1-1-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-gviz v1.18.1-1-deb_cv1
- version: 1.4.0
chgyi/bio 3.5.1
- version: 1.10.1
canaantt/notitia-ocpu latest
This is part of zager/notitia.
- version: 1.8.1
biocontainers/bioconductor-deseq2 v1.14.1-1-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-summarizedexperiment v1.4.0-2-deb_cv1
- version: 1.4.0
biocontainers/bioconductor-genomicfeatures v1.26.2-1-deb_cv1
- version: 1.4.0
chgyi/metaware_rna_denovo latest
- version: 1.12.0
dhspence/docker-manta 1.5.0
- version: 1.10.1
dhspence/docker-hiccompare latest
- version: 1.16.1
koki/sctensor-workshop sha-fa8c4cf
- version: 1.23.5
atttilacs/dsp_geomxtools latest
- version: 1.24.0
kcapd/wings-genomics latest
WINGS workflow system with software for genomics operations.
- version: 1.4.0
atttilacs/seurat_big latest
- version: 1.24.0
mirekphd/ml-cpu-r35-rdp 20180918
- version: 1.10.1
jafoltz/scclassify latest
- version: 1.24.0
crukmi/mesa main
- version: 1.27.3
testalabgh/downstream signac-1.4.0
- version: 1.24.0
mlepetit/ranalysis 3.3.4
- version: 1.22.0
tercen/flowsuite 0.0.4
- version: 1.20.0
dolphinnext/ont_variant_calling 1.0
- version: 1.28.0
scgfacility/rstudio-course22 v0.11
image used to run the course 2022
- version: 1.28.0
hdsu/etbii2023 latest
- version: 1.24.0
qdidiscoveryservices/quantiseqr v1
- version: 1.25.3
ccdlstaging/dr_common_tests 1.45.8
- version: 1.8.1
tercen/flowsom_operator 1.6.2
- version: 1.26.1