nfcore/nanoseq : dev

Nanopore demultiplexing, QC and alignment pipeline

Latest release: over 5 years ago - 9,909 downloads - 340 dependencies

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Dependencies

@PKGNAME@ @PKGVERSION@
@PKGNAME@ @VERSION@
AnnotationDbi 1.52.0
BH 1.72.0-3
BSgenome 1.58.0
Biobase 2.50.0
BiocFileCache 1.14.0
BiocGenerics 0.36.0
BiocParallel 1.24.0
Biostrings 2.58.0
DBI 1.1.0
DESeq2 1.30.0
DEXSeq 1.36.0
DRIMSeq 1.18.0
DelayedArray 0.16.0
GenomeInfoDb 1.26.0
GenomeInfoDbData 1.2.4
GenomicAlignments 1.26.0
GenomicFeatures 1.42.0
GenomicRanges 1.42.0
IRanges 2.24.0
MASS 7.3-53
Matrix 1.2-18
MatrixGenerics 1.2.0
R6 2.5.0
RColorBrewer 1.1-2
RCurl 1.98-1.2
RSQLite 2.2.1
Rcpp 1.0.5
RcppArmadillo 0.10.1.2.0
Rhtslib 1.22.0
Rsamtools 2.6.0
S4Vectors 0.28.0
SummarizedExperiment 1.20.0
XML 3.99-0.5
XVector 0.30.0
annotate 1.68.0
askpass 1.1
assertthat 0.2.1
backports 1.2.1
bambu 1.0.2
base 4.0.2
biomaRt 2.46.0
bit64 4.0.5
bit 4.0.4
bitops 1.0-6
blob 1.2.1
brio 1.1.0
callr 3.5.1
cli 2.2.0
codetools 0.2-18
colorspace 2.0-0
compiler 4.0.2
crayon 1.3.4
curl 4.3
data.table 1.13.4
datasets 4.0.2
dbplyr 2.0.0
desc 1.2.0
diffobj 0.3.2
digest 0.6.27
dplyr 1.0.2
edgeR 3.32.0
ellipsis 0.3.1
evaluate 0.14
fansi 0.4.1
farver 2.0.3
foreach 1.5.1
formatR 1.7
futile.logger 1.4.3
futile.options 1.0.1
genefilter 1.72.0
geneplotter 1.68.0
generics 0.1.0
ggplot2 3.3.2
glmnet 4.0-2
glue 1.4.2
grDevices 4.0.2
graphics 4.0.2
grid 4.0.2
gtable 0.3.0
hms 0.5.3
httr 1.4.2
hwriter 1.3.2
isoband 0.2.3
iterators 1.0.13
jsonlite 1.7.2
labeling 0.4.2
lambda.r 1.2.4
lattice 0.20-41
lifecycle 0.2.0
limma 3.46.0
locfit 1.5-9.4
magrittr 2.0.1
matrixStats 0.57.0
memoise 1.1.0
methods 4.0.2
mgcv 1.8-33
mime 0.9
munsell 0.5.0
nlme 3.1-150
openssl 1.4.3
org.testing.db 0.1
parallel 4.0.2
pillar 1.4.7
pkgbuild 1.2.0
pkgconfig 2.0.3
pkgload 1.1.0
plogr 0.2.0
plyr 1.8.6
praise 1.0.0
prettyunits 1.1.1
processx 3.4.5
progress 1.2.2
ps 1.5.0
purrr 0.3.4
rappdirs 0.3.1
rematch2 2.1.2
reshape2 1.4.4
rlang 0.4.9
rprojroot 2.0.2
rstudioapi 0.13
rtracklayer 1.50.0
scales 1.1.1
shape 1.4.5
snow 0.4-3
splines 4.0.2
stageR 1.12.0
statmod 1.4.35
stats4 4.0.2
stats 4.0.2
stringi 1.5.3
stringr 1.4.0
survival 3.2-7
sys 3.4
tcltk 4.0.2
testRcppClass 0.1
testRcppInterfaceExporter 0.1.0
testRcppInterfaceUser 0.1.0
testRcppModule 0.1
testRcppPackage 0.1.0
testthat 3.0.1
tibble 3.0.4
tidyselect 1.1.0
tools 4.0.2
translations 4.0.2
utf8 1.1.4
utils 4.0.2
vctrs 0.3.6
viridisLite 0.3.0
waldo 0.2.3
withr 2.3.0
xml2 1.3.2
xtable 1.8-4
zeallot 0.1.0
zlibbioc 1.36.0

debian/adduser 3.118
debian/apt 1.8.2
debian/base-files 10.3 deb10u3
debian/base-passwd 3.5.46
debian/bash 5.0-4
debian/bsdutils 1:2.33.1-0.1
debian/bzip2 1.0.6-9.2~deb10u1
debian/ca-certificates 20190110
debian/coreutils 8.30-3
debian/dash 0.5.10.2-5
debian/debconf 1.5.71
debian/debian-archive-keyring 2019.1
debian/debianutils 4.8.6.1
debian/diffutils 1:3.7-3
debian/dpkg 1.19.7
debian/e2fsprogs 1.44.5-1 deb10u3
debian/fdisk 2.33.1-0.1
debian/file 1:5.35-4 deb10u1
debian/findutils 4.6.0 git 20190209-2
debian/gcc-8-base 8.3.0-6
debian/git-man 1:2.20.1-2 deb10u1
debian/git 1:2.20.1-2 deb10u1
debian/gpgv 2.2.12-1 deb10u1
debian/grep 3.3-1
debian/gzip 1.9-3
debian/hostname 3.21
debian/init-system-helpers 1.56 nmu1
debian/krb5-locales 1.17-3
debian/less 487-0.1 b1
debian/libacl1 2.2.53-4
debian/libapr1 1.6.5-1 b1
debian/libaprutil1 1.6.1-4
debian/libapt-pkg5.0 1.8.2
debian/libattr1 1:2.4.48-4
debian/libaudit-common 1:2.8.4-3
debian/libaudit1 1:2.8.4-3
debian/libblkid1 2.33.1-0.1
debian/libbsd0 0.9.1-2
debian/libbz2-1.0 1.0.6-9.2~deb10u1
debian/libc-bin 2.28-10
debian/libc6 2.28-10
debian/libcap-ng0 0.7.9-2
debian/libcom-err2 1.44.5-1 deb10u3
debian/libcurl3-gnutls 7.64.0-4 deb10u1
debian/libdb5.3 5.3.28 dfsg1-0.5
debian/libdebconfclient0 0.249
debian/libedit2 3.1-20181209-1
debian/liberror-perl 0.17027-2
debian/libexpat1 2.2.6-2 deb10u1
debian/libext2fs2 1.44.5-1 deb10u3
debian/libfdisk1 2.33.1-0.1
debian/libffi6 3.2.1-9
debian/libgcc1 1:8.3.0-6
debian/libgcrypt20 1.8.4-5
debian/libgdbm-compat4 1.18.1-4
debian/libgdbm6 1.18.1-4
debian/libglib2.0-0 2.58.3-2 deb10u2
debian/libglib2.0-data 2.58.3-2 deb10u2
debian/libgmp10 2:6.1.2 dfsg-4
debian/libgnutls30 3.6.7-4 deb10u2
debian/libgpg-error0 1.35-1
debian/libgpm2 1.20.7-5
debian/libgssapi-krb5-2 1.17-3
debian/libhogweed4 3.4.1-1
debian/libice6 2:1.0.9-2
debian/libicu63 63.1-6
debian/libidn2-0 2.0.5-1 deb10u1
debian/libk5crypto3 1.17-3
debian/libkeyutils1 1.6-6
debian/libkrb5-3 1.17-3
debian/libkrb5support0 1.17-3
debian/libldap-2.4-2 2.4.47 dfsg-3 deb10u1
debian/libldap-common 2.4.47 dfsg-3 deb10u1
debian/liblz4-1 1.8.3-1
debian/liblzma5 5.2.4-1
debian/libmagic-mgc 1:5.35-4 deb10u1
debian/libmagic1 1:5.35-4 deb10u1
debian/libmount1 2.33.1-0.1
debian/libncurses6 6.1 20181013-2 deb10u2
debian/libncursesw6 6.1 20181013-2 deb10u2
debian/libnettle6 3.4.1-1
debian/libnghttp2-14 1.36.0-2 deb10u1
debian/libp11-kit0 0.23.15-2
debian/libpam-modules-bin 1.3.1-5
debian/libpam-modules 1.3.1-5
debian/libpam-runtime 1.3.1-5
debian/libpam0g 1.3.1-5
debian/libpcre2-8-0 10.32-5
debian/libpcre3 2:8.39-12
debian/libperl5.28 5.28.1-6
debian/libprocps7 2:3.3.15-2
debian/libpsl5 0.20.2-2
debian/libpython-stdlib 2.7.16-1
debian/libpython2-stdlib 2.7.16-1
debian/libpython2.7-minimal 2.7.16-2 deb10u1
debian/libpython2.7-stdlib 2.7.16-2 deb10u1
debian/libreadline7 7.0-5
debian/librtmp1 2.4 20151223.gitfa8646d.1-2
debian/libsasl2-2 2.1.27 dfsg-1 deb10u1
debian/libsasl2-modules-db 2.1.27 dfsg-1 deb10u1
debian/libsasl2-modules 2.1.27 dfsg-1 deb10u1
debian/libseccomp2 2.3.3-4
debian/libselinux1 2.8-1 b1
debian/libsemanage-common 2.8-2
debian/libsemanage1 2.8-2
debian/libsepol1 2.8-1
debian/libserf-1-1 1.3.9-7 b10
debian/libsm6 2:1.2.3-1
debian/libsmartcols1 2.33.1-0.1
debian/libsqlite3-0 3.27.2-3
debian/libss2 1.44.5-1 deb10u3
debian/libssh2-1 1.8.0-2.1
debian/libssl1.1 1.1.1d-0 deb10u2
debian/libstdc 6 8.3.0-6
debian/libsvn1 1.10.4-1 deb10u1
debian/libsystemd0 241-7~deb10u3
debian/libtasn1-6 4.13-3
debian/libtinfo6 6.1 20181013-2 deb10u2
debian/libudev1 241-7~deb10u3
debian/libunistring2 0.9.10-1
debian/libutf8proc2 2.3.0-1
debian/libuuid1 2.33.1-0.1
debian/libx11-6 2:1.6.7-1
debian/libx11-data 2:1.6.7-1
debian/libxau6 1:1.0.8-1 b2
debian/libxcb1 1.13.1-2
debian/libxdmcp6 1:1.1.2-3
debian/libxext6 2:1.3.3-1 b2
debian/libxml2 2.9.4 dfsg1-7 b3
debian/libxmuu1 2:1.1.2-2 b3
debian/libxrender1 1:0.9.10-1
debian/libzstd1 1.3.8 dfsg-3
debian/login 1:4.5-1.1
debian/lsb-base 10.2019051400
debian/mawk 1.3.3-17 b3
debian/mercurial-common 4.8.2-1 deb10u1
debian/mercurial 4.8.2-1 deb10u1
debian/mime-support 3.62
debian/mount 2.33.1-0.1
debian/ncurses-base 6.1 20181013-2 deb10u2
debian/ncurses-bin 6.1 20181013-2 deb10u2
debian/netbase 5.6
debian/openssh-client 1:7.9p1-10 deb10u2
debian/openssl 1.1.1d-0 deb10u2
debian/passwd 1:4.5-1.1
debian/patch 2.7.6-3 deb10u1
debian/perl-base 5.28.1-6
debian/perl-modules-5.28 5.28.1-6
debian/perl 5.28.1-6
debian/procps 2:3.3.15-2
debian/psmisc 23.2-1
debian/publicsuffix 20190415.1030-1
debian/python-minimal 2.7.16-1
debian/python2-minimal 2.7.16-1
debian/python2.7-minimal 2.7.16-2 deb10u1
debian/python2.7 2.7.16-2 deb10u1
debian/python2 2.7.16-1
debian/python 2.7.16-1
debian/readline-common 7.0-5
debian/sed 4.7-1
debian/sensible-utils 0.0.12
debian/shared-mime-info 1.10-1
debian/subversion 1.10.4-1 deb10u1
debian/sysvinit-utils 2.93-8
debian/tar 1.30 dfsg-6
debian/tzdata 2019c-0 deb10u1
debian/ucf 3.0038 nmu1
debian/util-linux 2.33.1-0.1
debian/wget 1.20.1-1.1
debian/x11-common 1:7.7 19
debian/xauth 1:1.0.10-1
debian/xdg-user-dirs 0.17-2
debian/xz-utils 5.2.4-1
debian/zlib1g 1:1.2.11.dfsg-1

java 11.0.8-internal 0-adhoc..src
python 3.7.6
python 3.8.6

mypy 0.770

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nfcore/nanoseq : dev

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