Ecosyste.ms: Docker

An open API service providing dependency metadata for docker images.

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 7

  • version: 1.28.0
Latest release: 12 months ago - 624,940 downloads - 550 dependencies
ccdlstaging/dr_downloaders 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 124,831 downloads - 1,028 dependencies
broadinstitute/terra-jupyter-aou 8bf6b13

  • version: 1.28.0, 1.24.0
Latest release: almost 2 years ago - 92,816 downloads - 4,112 dependencies
ccdlstaging/dr_affymetrix f30409aceba66e19235b21b4ca8899e318e02e30

  • version: 1.8.1
Latest release: about 1 year ago - 92,270 downloads - 1,220 dependencies
nfcore/methylseq dev

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel.

  • version: 1.22.0
Latest release: over 3 years ago - 92,677 downloads - 297 dependencies
ccdlstaging/dr_salmon f30409aceba66e19235b21b4ca8899e318e02e30

  • version: 1.8.1
Latest release: about 1 year ago - 57,229 downloads - 916 dependencies
nfcore/atacseq latest

A Docker container for the nf-core/atacseq pipeline.

  • version: 1.16.0
Latest release: over 2 years ago - 54,429 downloads - 352 dependencies
biocontainers/control-freec v11.5_cv1

  • version: 1.0.2
Latest release: almost 5 years ago - 52,130 downloads - 432 dependencies
nfcore/chipseq dev

A docker image for nf-core/chipseq

  • version: 1.18.1
Latest release: over 3 years ago - 50,176 downloads - 309 dependencies
nfcore/eager 2.5.0

A Docker image for the nf-core/eager pipeline.

  • version: 1.20.0
Latest release: about 1 year ago - 40,624 downloads - 738 dependencies
mirekphd/ml-cpu-r40-rs-cust 20230912

  • version: 1.30.2
Latest release: about 1 year ago - 21,613 downloads - 10,962 dependencies
dhspence/docker-genomic-analysis 122121

From Chris Miller's example

  • version: 1.16.1
Latest release: almost 3 years ago - 19,678 downloads - 1,294 dependencies
mirekphd/ml-cpu-r36-rs-cust latest

  • version: 1.8.0
Latest release: over 2 years ago - 13,673 downloads - 11,684 dependencies
ccdlstaging/dr_no_op 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 14,674 downloads - 894 dependencies
nfcore/ampliseq dev

A Docker image for nf-core/ampliseq.

  • version: 1.12.0
Latest release: almost 4 years ago - 10,364 downloads - 331 dependencies
mirekphd/ml-cpu-r36-base latest

  • version: 1.8.0
Latest release: over 2 years ago - 6,685 downloads - 12,259 dependencies
biocontainers/isee-galaxy v3.13_cv1.0.0

  • version: 1.23.1
Latest release: about 3 years ago - 3,660 downloads - 1,218 dependencies
ccdlstaging/dr_smasher 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 4,929 downloads - 884 dependencies
ccdlstaging/dr_illumina 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 3,448 downloads - 893 dependencies
patroonorg/patroondeps latest

  • version: 1.28.0
Latest release: over 1 year ago - 2,754 downloads - 1,677 dependencies
dhspence/docker-biscuit latest

  • version: 1.10.1
Latest release: almost 6 years ago - 1,935 downloads - 807 dependencies
ccdlstaging/dr_compendia 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 2,332 downloads - 877 dependencies
nfcore/airrflowreport dev

  • version: 1.28.0
Latest release: over 1 year ago - 994 downloads - 409 dependencies
nfcore/circrna dev

Workflow for analysis and miRNA target prediction analysis of circRNAs in RNA-Seq data.

  • version: 1.16.0
Latest release: about 2 years ago - 1,202 downloads - 654 dependencies
nfcore/sarek 2.7.2

A Docker container for the nf-core/sarek pipeline

  • version: 1.20.0
Latest release: over 2 years ago - 1,052,189 downloads - 607 dependencies
nfcore/slamseq dev

A docker image for nf-core/slamseq

  • version: 1.12.0
Latest release: over 3 years ago - 25,614 downloads - 354 dependencies
nfcore/hic dev

A docker container for the nf-core/hic pipeline.

  • version: 1.18.1
Latest release: about 3 years ago - 15,244 downloads - 257 dependencies
nfcore/nanoseq dev

Nanopore demultiplexing, QC and alignment pipeline

  • version: 1.20.0
Latest release: almost 4 years ago - 9,677 downloads - 340 dependencies
nfcore/scrnaseq dev

A Docker Container for the nf-core/scrnaseq pipeline.

  • version: 1.16.0
Latest release: over 3 years ago - 7,707 downloads - 423 dependencies
mirekphd/ml-cpu-r35-rs 20190201

  • version: 1.10.1
Latest release: almost 6 years ago - 762 downloads - 9,716 dependencies
dhspence/docker-homer latest

docker with chip-seq tool homer

  • version: 1.10.1
Latest release: almost 6 years ago - 702 downloads - 606 dependencies
nfcore/exoseq dev

A docker container for the ExoSeq pipeline

  • version: 1.10.1
Latest release: almost 6 years ago - 1,158 downloads - 616 dependencies
nfcore/lncpipe dev

A Docker image for nf-core/lncpipe

  • version: 1.10.1
Latest release: almost 6 years ago - 1,141 downloads - 413 dependencies
seglh/exomedepth f4716ad

  • version: 1.26.1
Latest release: 12 months ago - 928 downloads - 548 dependencies
veitveit/vsclust release-1.2.1

For more details, see https://bitbucket.org/veitveit/vsclust

  • version: 1.28.0
Latest release: over 1 year ago - 445 downloads - 1,148 dependencies
dhspence/docker-sicer latest

  • version: 1.10.1
Latest release: almost 6 years ago - 765 downloads - 1,147 dependencies
qdidiscoveryservices/limma-voom 4.2.0

  • version: 1.26.1
Latest release: over 2 years ago - 1,002 downloads - 1,382 dependencies
qdidiscoveryservices/cellranger7.0.1_py3_r4 v1.2.2

  • version: 1.24.0
Latest release: about 1 year ago - 2,811 downloads - 1,464 dependencies
dhspence/docker-basestation latest

  • version: 1.10.1
Latest release: over 5 years ago - 308 downloads - 1,132 dependencies
qdidiscoveryservices/py3_cellranger 6.1.2

  • version: 1.18.1
Latest release: about 3 years ago - 302 downloads - 1,375 dependencies
dhspence/docker-dss latest

  • version: 1.16.1
Latest release: over 4 years ago - 367 downloads - 1,127 dependencies
biocontainers/bioconductor-cummerbund v2.16.0-2-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 502 downloads - 576 dependencies
biocontainers/bioconductor-bsgenome v1.42.0-2-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 533 downloads - 430 dependencies
biocontainers/bioconductor-variantannotation v1.20.2-1b1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 529 downloads - 457 dependencies
biocontainers/bioconductor-ensembldb v1.6.2-1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 522 downloads - 498 dependencies
biocontainers/bioconductor-shortread v1.32.0-1b1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 522 downloads - 431 dependencies
tercen/runtime-flowsuite 3.15-4

  • version: 1.26.1
Latest release: about 2 years ago - 353 downloads - 1,641 dependencies
cimendes/splicing-pipelines-nf 3.1.ubuntu

  • version: 1.22.0
Latest release: almost 2 years ago - 237 downloads - 227 dependencies
biocontainers/bioconductor-genomicalignments v1.10.0-1b1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 520 downloads - 423 dependencies
biocontainers/bioconductor-biovizbase v1.22.0-2-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 477 downloads - 568 dependencies
koki/sctensor-experiments 20220208

  • version: 1.24.0
Latest release: almost 3 years ago - 206 downloads - 2,071 dependencies
evolbioinfo/deseq2 v1.28.1

  • version: 1.18.2
Latest release: about 4 years ago - 206 downloads - 452 dependencies
qdidiscoveryservices/scrna_downstream 1.1

  • version: 1.22.0
Latest release: almost 3 years ago - 354 downloads - 1,716 dependencies
recetox/ramclustr 1.1.0-recetox0

  • version: 1.18.2
Latest release: about 4 years ago - 191 downloads - 593 dependencies
koki/biocdev 20230818

  • version: 1.31.1
Latest release: over 1 year ago - 201 downloads - 1,504 dependencies
anand7899/rmarkdown latest

  • version: 1.28.0
Latest release: about 2 years ago - 262 downloads - 766 dependencies
prismcmap/sushi develop

  • version: 1.20.0
Latest release: 10 months ago - 221 downloads - 723 dependencies
hoonbiolab/hmftools v1.1

  • version: 1.22.0
Latest release: about 3 years ago - 1,211 downloads - 693 dependencies
qdidiscoveryservices/bam_to_10x_counts latest

  • version: 1.24.0
Latest release: about 2 years ago - 172 downloads - 962 dependencies
biocontainers/bioconductor-rtracklayer v1.34.1-1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 160 downloads - 427 dependencies
biocontainers/bioconductor-gviz v1.18.1-1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 156 downloads - 572 dependencies
chgyi/bio 3.5.1

  • version: 1.10.1
Latest release: about 6 years ago - 158 downloads - 1,077 dependencies
canaantt/notitia-ocpu latest

This is part of zager/notitia.

  • version: 1.8.1
Latest release: almost 7 years ago - 153 downloads - 633 dependencies
biocontainers/bioconductor-deseq2 v1.14.1-1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 155 downloads - 523 dependencies
biocontainers/bioconductor-summarizedexperiment v1.4.0-2-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 141 downloads - 407 dependencies
biocontainers/bioconductor-genomicfeatures v1.26.2-1-deb_cv1

  • version: 1.4.0
Latest release: over 6 years ago - 140 downloads - 453 dependencies
chgyi/metaware_rna_denovo latest

  • version: 1.12.0
Latest release: over 5 years ago - 132 downloads - 2,095 dependencies
dhspence/docker-manta 1.5.0

  • version: 1.10.1
Latest release: almost 6 years ago - 126 downloads - 1,191 dependencies
dhspence/docker-hiccompare latest

  • version: 1.16.1
Latest release: over 3 years ago - 113 downloads - 1,271 dependencies
koki/sctensor-workshop sha-fa8c4cf

  • version: 1.23.5
Latest release: about 3 years ago - 111 downloads - 2,087 dependencies
atttilacs/dsp_geomxtools latest

  • version: 1.24.0
Latest release: about 2 years ago - 114 downloads - 871 dependencies
kcapd/wings-genomics latest

WINGS workflow system with software for genomics operations.

  • version: 1.4.0
Latest release: about 4 years ago - 103 downloads - 1,468 dependencies
atttilacs/seurat_big latest

  • version: 1.24.0
Latest release: almost 2 years ago - 495 downloads - 997 dependencies
mirekphd/ml-cpu-r35-rdp 20180918

  • version: 1.10.1
Latest release: about 6 years ago - 93 downloads - 9,486 dependencies
jafoltz/scclassify latest

  • version: 1.24.0
Latest release: almost 2 years ago - 90 downloads - 1,079 dependencies
crukmi/mesa main

  • version: 1.27.3
Latest release: about 2 years ago - 91 downloads - 1,326 dependencies
testalabgh/downstream signac-1.4.0

  • version: 1.24.0
Latest release: over 1 year ago - 485 downloads - 3,517 dependencies
mlepetit/ranalysis 3.3.4

  • version: 1.22.0
Latest release: about 2 years ago - 79 downloads - 2,131 dependencies
tercen/flowsuite 0.0.4

  • version: 1.20.0
Latest release: over 2 years ago - 99 downloads - 1,512 dependencies
dolphinnext/ont_variant_calling 1.0

  • version: 1.28.0
Latest release: almost 2 years ago - 80 downloads - 494 dependencies
scgfacility/rstudio-course22 v0.11

image used to run the course 2022

  • version: 1.28.0
Latest release: almost 2 years ago - 75 downloads - 382 dependencies
hdsu/etbii2023 latest

  • version: 1.24.0
Latest release: almost 2 years ago - 73 downloads - 358 dependencies
qdidiscoveryservices/quantiseqr v1

  • version: 1.25.3
Latest release: over 2 years ago - 65 downloads - 1,201 dependencies
ccdlstaging/dr_common_tests 549216c6fa7f6c80a5d78287c8814330f150428c

  • version: 1.8.1
Latest release: 12 months ago - 710 downloads - 784 dependencies
tercen/flowsom_operator 1.6.0

  • version: 1.26.1
Latest release: almost 2 years ago - 105 downloads - 1,563 dependencies