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Package Usage : cran : ShortRead

Explore the latest package usage data for ShortRead in the cran ecosystem, including detailed information on package dependencies and their usage.

Total dependents: 76
Total downloads: 150,021
Showing first 100 dependents

More details on packages.ecosyste.ms - JSON

robertplayer/scidap-qiime2 stable

  • version: 1.56.0
Latest release: over 2 years ago - 34 downloads - 527 dependencies
eppicenter/mad4hatter sha-cb4911b

  • version: 1.58.0
Latest release: 2 months ago - 821 downloads - 739 dependencies
prismcmap/sushi v0.0.2

  • version: 1.48.0
Latest release: almost 4 years ago - 1,331 downloads - 723 dependencies
globusgenomics/picrust 1.0

  • version: 1.52.0
Latest release: almost 3 years ago - 129 downloads - 595 dependencies
intelliseqngs/bioconductor r-coverage-stats_v0.1

  • version: 1.44.0
Latest release: almost 6 years ago - 22 downloads - 185 dependencies
tariship/dev_sync_directories latest

  • version: 1.56.1
Latest release: about 2 years ago - 379 downloads - 421 dependencies
crukcibioinformatics/sequencingbase 9.3.4

  • version: 1.64.0
Latest release: 9 months ago - 323 downloads - 1,183 dependencies
prismcmap/base-clue-pseq v0.0.1

  • version: 1.48.0
Latest release: about 4 years ago - 116 downloads - 318 dependencies
sebrauschert/amplicon_pipeline v0.3.2

A pipeline for amplicon sequencing analysis of marine fish

  • version: 1.58.0
Latest release: over 2 years ago - 332 downloads - 571 dependencies
mattjmeier/r-odaf-hc-prod latest

  • version: 1.56.0
Latest release: almost 3 years ago - 50 downloads - 897 dependencies
commander121/rmarkdown 4.4.0d-b4

  • version: 1.58.0
Latest release: 9 months ago - 907 downloads - 1,625 dependencies
benolson/r_dada2_for_ris latest

  • version: 1.56.1
Latest release: over 2 years ago - 34 downloads - 657 dependencies
mfsentma/atacseq latest

  • version: 1.52.0
Latest release: over 2 years ago - 34 downloads - 852 dependencies
bac3/microbiome latest

16S rRNA gene meta-barcoding NGS data analysis app - microbioma batterico. App streamlit.

  • version: 1.56.0
Latest release: over 2 years ago - 190 downloads - 752 dependencies
fallingstar10/hbsigrocker latest

  • version: 1.58.0
Latest release: over 2 years ago - 256 downloads - 1,223 dependencies
dhspence/docker-manta 1.5.0

  • version: 1.38.0
Latest release: almost 7 years ago - 233 downloads - 1,191 dependencies
mattjmeier/r-odaf-hc latest

Under Development. Containerized version of the R-ODAF Health Canada Pipeline.

  • version: 1.56.0
Latest release: almost 3 years ago - 33 downloads - 598 dependencies
andrewatmp/qiime_unzip latest

  • version: 1.56.0
Latest release: over 2 years ago - 151 downloads - 598 dependencies
indraniel/chip-pipeline-annotation v1

  • version: 1.56.1
Latest release: over 2 years ago - 278 downloads - 218 dependencies
gesiscss/binder-mortonjt-2dq2stats-2dworkshops-912d21 82c8b562545acab37a854f097c33806fa7c2a4b3

  • version: 1.40.0
Latest release: over 4 years ago - 35 downloads - 1,679 dependencies
alexsickler/open-pedcan latest

  • version: 1.44.3
Latest release: almost 3 years ago - 219 downloads - 864 dependencies
emersonchao/dsc180b latest

  • version: 1.56.0
Latest release: almost 3 years ago - 62 downloads - 2,266 dependencies
shiramaty/qiime2-sratools latest

  • version: 1.52.0
Latest release: almost 3 years ago - 24 downloads - 319 dependencies
pauffret/peak-calling-box 1.0

  • version: 1.44.0
Latest release: almost 3 years ago - 20 downloads - 212 dependencies
lorentzb/srs 2.0

  • version: 1.40.0
Latest release: over 2 years ago - 78 downloads - 269 dependencies
mattjmeier/r-odaf-hc-base latest

  • version: 1.56.0
Latest release: almost 3 years ago - 20 downloads - 598 dependencies
omicschef/epigenomechef v1.1.5

  • version: 1.58.0
Latest release: over 1 year ago - 414 downloads - 1,066 dependencies
jlphillips/csci 2025-08-08-p2

MTSU Department of Computer Science Stack

  • version: 1.56.0
Latest release: 2 months ago - 1,863 downloads - 3,823 dependencies
sebimer/samba-v4-qiime2 2024.2

  • version: 1.56.0
Latest release: over 1 year ago - 246 downloads - 583 dependencies
almahmoud/terra-jupyter bioc

  • version: 1.54.0
Latest release: about 3 years ago - 73 downloads - 2,217 dependencies
bioedge/edge_24_1_ubuntu18 20231115

  • version: 1.56.0
Latest release: about 2 years ago - 155 downloads - 2,569 dependencies
jorgeamaya/ci_barcode_terra_dada2_iseq v1

  • version: 1.58.0
Latest release: over 2 years ago - 41 downloads - 483 dependencies
chgyi/qiime2 23.09

  • version: 1.40.0
Latest release: almost 2 years ago - 50 downloads - 271 dependencies
qdidiscoveryservices/diffbind latest

  • version: 1.58.0
Latest release: over 2 years ago - 44 downloads - 526 dependencies
kumalpha/qiime2-core latest

  • version: 1.48.0
Latest release: almost 3 years ago - 36 downloads - 420 dependencies
madhu99/sb6 latest

  • version: 1.56.1
Latest release: almost 3 years ago - 14 downloads - 666 dependencies
cgrlab/qiime2 2023.5

  • version: 1.56.0
Latest release: over 2 years ago - 84 downloads - 526 dependencies
shl198/rna_ppl latest

  • version: 1.54.0
Latest release: almost 3 years ago - 24 downloads - 2,099 dependencies
gesiscss/binder-r2d-g5b5b759-bassiousmaximus-2dbinder-2dr-2dgus-cfe967 f0376d46edceebca7d36de69b94f160a53a7ff78

  • version: 1.48.0
Latest release: over 2 years ago - 32 downloads - 2,152 dependencies
ycli1995/bioinfo_dev 1.1.0

  • version: 1.58.0
Latest release: over 1 year ago - 185 downloads - 4,337 dependencies
wyangwu/r4.1.2 latest

  • version: 1.52.0
Latest release: over 2 years ago - 93 downloads - 827 dependencies
wesdorp/aws_dna latest

  • version: 1.56.1
Latest release: over 2 years ago - 16 downloads - 563 dependencies
weishwu/diffbind 3.6.5

  • version: 1.54.0
Latest release: almost 3 years ago - 31 downloads - 1,507 dependencies
wlc27/dcanr v1

  • version: 1.56.1
Latest release: almost 3 years ago - 94 downloads - 1,681 dependencies
sharvaribatchx/dada2-filter-learn-errors latest

  • version: 1.52.0
Latest release: over 2 years ago - 14 downloads - 536 dependencies
preethiilumina/diffbind 1.5.1

fixed genome name

  • version: 1.56.1
Latest release: 12 months ago - 319 downloads - 626 dependencies
gesiscss/binder-r2d-g5b5b759-natpombubpa-2damptk-5f1-2e5-2e4-904cbc b7b2357f6670556e582166033b738136fa103199

  • version: 1.56.0
Latest release: over 2 years ago - 52 downloads - 1,700 dependencies
weishwu/systempiper 12022022

  • version: 1.54.0
Latest release: about 3 years ago - 29 downloads - 1,383 dependencies
ntobias85/abe_repo rbuild_reports_1.0.1

  • version: 1.42.0
Latest release: over 1 year ago - 311 downloads - 1,339 dependencies
mapostolides/test12345 latest

  • version: 1.44.1
Latest release: over 2 years ago - 12 downloads - 566 dependencies
dhspence/docker-genomic-analysis 122121

From Chris Miller's example

  • version: 1.44.3
Latest release: almost 4 years ago - 19,986 downloads - 1,294 dependencies
mirekphd/ml-cpu-r36-rs-cust latest

  • version: 1.36.0
Latest release: over 3 years ago - 19,292 downloads - 11,684 dependencies
nfcore/ampliseq 1.2.0

A Docker image for nf-core/ampliseq.

  • version: 1.40.0
Latest release: almost 5 years ago - 10,823 downloads - 331 dependencies
mirekphd/ml-cpu-r36-base latest

  • version: 1.36.0
Latest release: over 3 years ago - 10,855 downloads - 12,259 dependencies
shashankti/bioc_docker v1

  • version: 1.57.1
Latest release: almost 3 years ago - 52 downloads - 1,350 dependencies
broadinstitute/terra-jupyter-aou 2.1.13

  • version: 1.52.0, 1.56.1
Latest release: almost 3 years ago - 97,191 downloads - 4,112 dependencies
vmikk/nextits 1.1.0

  • version: 1.66.0
Latest release: 3 months ago - 304 downloads - 627 dependencies
tipsarin/rstudio 4.1.3

  • version: 1.52.0
Latest release: over 3 years ago - 60 downloads - 981 dependencies
dhspence/docker-vep 93

  • version: 1.38.0
Latest release: almost 7 years ago - 87 downloads - 1,191 dependencies
jorgeamaya/dada2_terra_iseq v1

  • version: 1.58.0
Latest release: over 2 years ago - 392 downloads - 967 dependencies
mbwali/jupyterlab qiime2023

  • version: 1.56.0
Latest release: over 2 years ago - 176 downloads - 1,941 dependencies
mirekphd/ml-cpu-r36-rs 20200131

  • version: 1.36.0
Latest release: almost 6 years ago - 68 downloads - 10,669 dependencies
etretiakov/workbench-session-complete jammy-2024.09.19-custom-12.9

  • version: 1.58.0
Latest release: about 1 year ago - 1,187 downloads - 6,961 dependencies
leepc12/test-jupyterhub v0.2.0

test-jupyterhub

  • version: 1.56.1
Latest release: over 2 years ago - 132 downloads - 1,857 dependencies
pipecraft/vsearch_dada2 0

  • version: 1.58.0
Latest release: about 2 years ago - 564 downloads - 785 dependencies
mirekphd/ml-cpu-r35-rdp 20180918

  • version: 1.38.0
Latest release: about 7 years ago - 312 downloads - 9,486 dependencies
mirekphd/ml-cpu-r35-rs 20190201

  • version: 1.36.0
Latest release: almost 7 years ago - 1,669 downloads - 9,716 dependencies
dhspence/docker-sicer latest

  • version: 1.38.0
Latest release: almost 7 years ago - 813 downloads - 1,147 dependencies
omicsclass/metagenomics latest

  • version: 1.52.0
Latest release: about 2 years ago - 75 downloads - 1,493 dependencies
lroser/databricksbio latest

  • version: 1.58.0
Latest release: over 2 years ago - 95 downloads - 975 dependencies
ethill/qiime2 latest

docker container for qiime2

  • version: 1.56.0
Latest release: almost 3 years ago - 20 downloads - 1,935 dependencies
chunjiesamliu/scmocha latest

  • version: 1.58.0
Latest release: over 2 years ago - 74 downloads - 1,258 dependencies
paulotaugc/16scan-metagenomics v2

  • version: 1.52.0
Latest release: over 2 years ago - 129 downloads - 776 dependencies
etretiakov/rocker-session latest

  • version: 1.58.0
Latest release: over 2 years ago - 78 downloads - 2,565 dependencies
nucleoz/cnvplotr3 latest

  • version: 1.36.1
Latest release: over 2 years ago - 44 downloads - 478 dependencies
biocontainers/bioconductor-shortread v1.32.0-1b1-deb_cv1

  • version: 1.32.0
Latest release: over 7 years ago - 533 downloads - 431 dependencies
dhspence/docker-basestation latest

  • version: 1.38.0
Latest release: over 6 years ago - 351 downloads - 1,132 dependencies
alesmaver/scramble2 latest

  • version: 1.44.3
Latest release: over 2 years ago - 2,947 downloads - 1,116 dependencies
andrewatmp/testf latest

  • version: 1.56.0
Latest release: over 2 years ago - 468 downloads - 536 dependencies