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sebrauschert/amplicon_pipeline : v0.3.2

A pipeline for amplicon sequencing analysis of marine fish

Latest release: over 1 year ago - 60 downloads - 571 dependencies

JSON

Dependencies

@PKGNAME@ @VERSION@
BH 1.81.0-1
Biobase 2.60.0
BiocGenerics 0.46.0
BiocManager 1.30.20
BiocParallel 1.34.2
BiocVersion 3.17.1
Biostrings 2.68.1
DBI 1.1.3
DECIPHER 2.28.0
DelayedArray 0.26.3
GenomeInfoDb 1.36.0
GenomeInfoDbData 1.2.10
GenomicAlignments 1.36.0
GenomicRanges 1.52.0
IRanges 2.34.0
KernSmooth 2.23-20
Lahman 11.0-0
MASS 7.3-58.4
Matrix 1.5-4
MatrixGenerics 1.12.0
R6 2.5.1
RColorBrewer 1.1-3
RCurl 1.98-1.12
RMariaDB 1.2.2
RPostgres 1.4.5
RSQLite 2.3.1
Rcpp 1.0.10
RcppArmadillo 0.12.4.0.0
RcppEigen 0.3.3.9.3
RcppParallel 5.1.7
Rhdf5lib 1.22.0
Rhtslib 2.2.0
Rsamtools 2.16.0
S4Arrays 1.0.4
S4Vectors 0.38.1
ShortRead 1.58.0
SummarizedExperiment 1.30.1
XVector 0.40.0
ade4 1.7-22
ape 5.7-1
arrow 12.0.0
askpass 1.1
assertthat 0.2.1
backports 1.4.1
base64enc 0.1-3
base 4.3.0
biomformat 1.28.0
bit64 4.0.5
bit 4.0.5
bitops 1.0-7
blob 1.2.4
boot 1.3-28.1
brew 1.0-8
brio 1.1.3
broom 1.0.4
bslib 0.4.2
cachem 1.0.8
callr 3.7.3
cellranger 1.1.0
class 7.3-21
cli 3.6.1
clipr 0.8.0
cluster 2.1.4
codetools 0.2-19
colorspace 2.1-0
commonmark 1.9.0
compiler 4.3.0
conflicted 1.2.0
cpp11 0.4.3
crayon 1.5.2
credentials 1.3.2
curl 5.0.0
dada2 1.28.0
data.table 1.14.8
datasets 4.3.0
dbplyr 2.3.2
deldir 1.0-9
desc 1.4.2
devtools 2.4.5
diffobj 0.3.5
digest 0.6.31
docopt 0.7.1
downlit 0.4.2
dplyr 1.1.2
dtplyr 1.3.1
duckdb 0.7.1-1
ellipsis 0.3.2
evaluate 0.21
fansi 1.0.4
farver 2.1.1
fastmap 1.1.1
fastmatch 1.1-3
fontawesome 0.5.1
forcats 1.0.0
foreach 1.5.2
foreign 0.8-84
formatR 1.14
fs 1.6.2
fst 0.9.8
fstcore 0.9.14
futile.logger 1.4.3
futile.options 1.0.1
gargle 1.4.0
generics 0.1.3
gert 1.9.2
getopt 1.20.3
ggplot2 3.4.2
gh 1.4.0
gitcreds 0.1.2
glue 1.6.2
googledrive 2.1.0
googlesheets4 1.1.0
grDevices 4.3.0
graphics 4.3.0
grid 4.3.0
gtable 0.3.3
haven 2.5.2
highr 0.10
hms 1.1.3
htmltools 0.5.5
htmlwidgets 1.6.2
httpuv 1.6.11
httr2 0.2.3
httr 1.4.6
hwriter 1.3.2.1
ids 1.0.1
igraph 1.4.3
ini 0.3.1
interp 1.1-4
isoband 0.2.7
iterators 1.0.14
jpeg 0.1-10
jquerylib 0.1.4
jsonlite 1.8.4
knitr 1.42
labeling 0.4.2
lambda.r 1.2.4
later 1.3.1
lattice 0.21-8
latticeExtra 0.6-30
lifecycle 1.0.3
littler 0.3.18
lubridate 1.9.2
lulu 0.1.0
magrittr 2.0.3
matrixStats 0.63.0
memoise 2.0.1
methods 4.3.0
mgcv 1.8-42
mime 0.12
miniUI 0.1.1.1
modelr 0.1.11
multtest 2.56.0
munsell 0.5.0
nlme 3.1-162
nnet 7.3-18
nycflights13 1.0.2
openssl 2.0.6
optparse 1.7.3
parallel 4.3.0
permute 0.9-7
phangorn 2.11.1
phyloseq 1.44.0
pillar 1.9.0
pixmap 0.4-12
pkgbuild 1.4.0
pkgconfig 2.0.3
pkgdown 2.0.7
pkgload 1.3.2
plogr 0.2.0
plyr 1.8.8
png 0.1-8
praise 1.0.0
prettyunits 1.1.1
processx 3.8.1
profvis 0.3.8
progress 1.2.2
promises 1.2.0.1
ps 1.7.5
purrr 1.0.1
quadprog 1.5-8
ragg 1.2.5
rappdirs 0.3.3
rcmdcheck 1.4.0
readr 2.1.4
readxl 1.4.2
rematch2 2.1.2
rematch 1.0.1
remotes 2.4.2
reprex 2.0.2
reshape2 1.4.4
rhdf5 2.44.0
rhdf5filters 1.12.1
rlang 1.1.1
rmarkdown 2.21
roxygen2 7.2.3
rpart 4.1.19
rprojroot 2.0.3
rstudioapi 0.14
rversions 2.1.2
rvest 1.0.3
sass 0.4.6
scales 1.2.1
selectr 0.4-2
sessioninfo 1.2.2
shiny 1.7.4
snow 0.4-4
sourcetools 0.1.7-1
sp 1.6-0
spatial 7.3-16
splines 4.3.0
stats4 4.3.0
stats 4.3.0
stringi 1.7.12
stringr 1.5.0
survival 3.5-5
sys 3.4.1
systemfonts 1.0.4
tcltk 4.3.0
testRcppAttributePackage 1.0
testRcppClass 0.1
testRcppInterfaceExporter 0.1.0
testRcppInterfaceUser 0.1.0
testRcppModule 0.1
testRcppPackage 0.1.0
testthat 3.1.8
textshaping 0.3.6
tibble 3.2.1
tidyr 1.3.0
tidyselect 1.2.0
tidyverse 2.0.0
timechange 0.2.0
tinytex 0.45
tools 4.3.0
translations 4.3.0
tzdb 0.3.0
urlchecker 1.0.1
usethis 2.1.6
utf8 1.2.3
utils 4.3.0
uuid 1.1-0
vctrs 0.6.2
vegan 2.6-4
viridisLite 0.4.2
vroom 1.6.3
waldo 0.5.1
whisker 0.4.1
withr 2.5.0
xfun 0.39
xml2 1.3.4
xopen 1.0.0
xtable 1.8-4
yaml 2.3.7
zip 2.3.0
zlibbioc 1.46.0

bash 5.1.16
python 2.7.18
python 3.10.0
python 3.10.4
python 3.10.6
python 3.9.12

edirect (devel)
github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af
github.com/biogo/biogo v1.0.3
github.com/biogo/hts v1.4.3
github.com/bsipos/thist v1.0.0
github.com/cespare/xxhash/v2 v2.1.2
github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8
github.com/dustin/go-humanize v1.0.0
github.com/edsrzf/mmap-go v1.0.0
github.com/evanw/esbuild v0.0.0-20220830001118-78a1e00b2e69
github.com/fatih/color v1.12.0
github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90
github.com/fsnotify/fsnotify v1.5.1
github.com/gedex/inflector v0.0.0-20170307190818-16278e9db813
github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0
github.com/iafan/cwalk v0.0.0-20210125030640-586a8832a711
github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5
github.com/klauspost/compress v1.11.4
github.com/klauspost/compress v1.13.4
github.com/klauspost/cpuid v1.3.1
github.com/klauspost/pgzip v1.2.5
github.com/logrusorgru/aurora v2.0.3 incompatible
github.com/mattn/go-colorable v0.1.8
github.com/mattn/go-isatty v0.0.12
github.com/mattn/go-isatty v0.0.13
github.com/mattn/go-runewidth v0.0.13
github.com/mitchellh/go-homedir v1.1.0
github.com/pbnjay/memory v0.0.0-20210728143218-7b4eea64cf58
github.com/pkg/errors v0.9.1
github.com/rainycape/unidecode v0.0.0-20150907023854-cb7f23ec59be
github.com/rivo/uniseg v0.2.0
github.com/shenwei356/bio v0.0.0-20201213090627-18e3e643a476
github.com/shenwei356/bio v0.3.0
github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403
github.com/shenwei356/breader v0.1.0
github.com/shenwei356/breader v0.3.0
github.com/shenwei356/bwt v0.5.1
github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba
github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d
github.com/shenwei356/seqkit (devel)
github.com/shenwei356/taxonkit (devel)
github.com/shenwei356/unikmer v0.17.1
github.com/shenwei356/util v0.3.0
github.com/shenwei356/util v2020.12.31 incompatible
github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992
github.com/shenwei356/xopen v0.1.0
github.com/smallfish/simpleyaml v0.1.0
github.com/spf13/cobra v1.1.1
github.com/spf13/cobra v1.2.1
github.com/spf13/pflag v1.0.5
github.com/surgebase/porter2 v0.0.0-20150829210152-56e4718818e8
github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939
github.com/twotwotwo/sorts v0.0.0-20160814051341-bf5c1f2b8553
github.com/will-rowe/nthash v0.3.0
golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9
golang.org/x/image v0.0.0-20190802002840-cff245a6509b
golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae
golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c
golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8
golang.org/x/text v0.3.7
gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b
gopkg.in/yaml.v2 v2.4.0
stdlib 1.16beta1
stdlib 1.17
stdlib 1.19

US_export_policy:US_export_policy *
charsets:charsets *
cisd-jhdf5:cisd-jhdf5 *
cldrdata:cldrdata *
com.sun:jce 1.8.0_152
com.sun:sunec 1.8.0_152
com.sun:sunjce_provider 1.8.0_152
com.sun:sunpkcs11 1.8.0_152
commons-io:commons-io 1.4
commons-lang:commons-lang 2.4
dnsns:dnsns *
dt:dt *
gettext:gettext *
jaccess:jaccess *
jbzip2:jbzip2 0.9
jconsole:jconsole *
jfxrt:jfxrt *
jfxswt:jfxswt *
jsse:jsse 1.8.0_152-release
libintl:libintl 0.21
local_policy:local_policy *
localedata:localedata *
management-agent:management-agent *
nashorn:nashorn 1.8.0_152-release-1056-b12
resources:resources 1.8.0_152-release
rt:rt 1.8.0_152-release
sa-jdi:sa-jdi *
sam:sam 1.103
tools:tools *
zipfs:zipfs 1.8.0_152-release

bootstrap-accessibility-plugin 1.0.6
bootstrap-colorpicker 3.4.0
bootstrap-sass 3.4.1
bootstrap 4.6.0
bootstrap 5.2.2
bootswatch 3.4.1
bootswatch 4.6.0
bootswatch 5.2.2

Automat 0.7.0
Babel 2.6.0
Babel 2.8.0
Bottleneck 1.3.4
CherryPy 17.1.0
CherryPy 17.2.0
CherryPy 17.2.1.dev1 gb6d8061f
Deprecated 1.2.13
Django 1.11.15
Django 2.1
ExifRead 2.3.2
Flask 2.0.1
Jinja2 3.0.3
MarkupSafe 2.0.1
Pillow 9.0.1
PyDispatcher 2.0.5
PyGObject 3.42.1
PyGithub 1.55
PyHamcrest 1.9.0
PyJWT 1.6.4
PyJWT 2.3.0
PyNaCl 1.5.0
PySocks 1.6.8
PySocks 1.7.1
PyYAML 5.4.1
Scrapy 1.5.0
Scrapy 1.5.1
SecretStorage 3.3.1
Twisted 18.7.0
Werkzeug 2.0.2
Whoosh 2.7.4
annexremote 1.6.0
apipkg 2.0.0
appdirs 1.4.4
argcomplete 1.8.1
argparse 1.2.1
asn1crypto 0.24.0
attrs 18.1.0
attrs 21.4.0
backports.functools-lru-cache 1.5
backports.pdb 1.0.2
backports.shutil-which 3.5.1
backports.weakref 1.0.post1
boto 2.49.0
brotlipy 0.7.0
certifi 2018.08.24
certifi 2020.6.20
certifi 2022.5.18.1
certifi 2023.5.7
cffi 1.11.5
cffi 1.15.1
chardet 3.0.4
chardet 4.0.0
charset-normalizer 2.0.4
cheroot 6.4.0
click 8.0.3
colorama 0.4.4
conda-package-handling 2.1.0
conda 4.12.0
conda_package_streaming 0.8.0
configparser 3.5.0
constantly 15.1.0
cryptography 2.3.1
cryptography 3.4.8
cryptography 39.0.1
cssselect 1.0.3
cutadapt 4.1
dask 0.18.2
dask 0.18.2 33.g0fca28e4
datalad 0.15.5
dbus-python 1.2.18
distro 1.7.0
django-phonenumber-field 2.0.0
django-phonenumber-field 2.0.1
django-twilio 0.9.2
dnaio 0.10.0
dnspython 2.1.0
entrypoints 0.2.3
enum34 1.1.6
fasteners 0.14.1
flask 0.10.1
functools32 3.2.3.post2
future 0.18.2
h5py 2.8.0
hdf5storage 0.1.15
html5lib 1.1
httpretty 1.1.4
humanize 0.0.0
hyperlink 18.0.0
idna 2.7
idna 3.3
idna 3.4
impacket 0.9.24
importlib-metadata 4.6.4
incremental 17.5.0
iniconfig 1.1.1
ipaddress 1.0.22
isal 1.1.0
iso8601 1.0.2
itsdangerous 2.1.0
jaraco.functools 1.20
jeepney 0.7.1
jsmin 3.0.0
keyring 13.2.1
keyring 23.5.0
keyrings.alt 4.1.0
ldap3 2.8.1
ldapdomaindump 0.9.3
linecache2 1.0.0
lxml 4.2.4
mkl-fft 1.3.1
mkl-random 1.2.2
mkl-service 2.4.0
mock 4.0.3
monotonic 1.6
more-itertools 4.3.0
more-itertools 8.10.0
msgpack 1.0.3
mutagen 1.45.1
nose 1.3.7
numexpr 2.7.3
numpy 1.15.0
numpy 1.15.1
numpy 1.22.3
olefile 0.46
packaging 21.3
pandas 1.4.2
parsel 1.5.0
patool 1.12
pbr 5.8.0
phonenumbers 8.9.11
phonenumbers 8.9.12
phonenumberslite 8.9.10
pip 18.0
pip 21.2.4
pip 23.1.2
pip 8.1.2
pluggy 0.7.1
pluggy 1.0.0
portend 2.3
py 1.11.0
py 1.5.4
py 1.6.0
pyOpenSSL 18.0.0
pyOpenSSL 21.0.0
pyOpenSSL 23.0.0
pyasn1-modules 0.2.2
pyasn1 0.4.4
pyasn1 0.4.8
pycosat 0.6.4
pycparser 2.18
pycparser 2.21
pycryptodomex 3.11.0
pyparsing 2.4.7
pyparsing 3.0.4
pyperclip 1.8.2
pytaxonkit 0.7.2
pytest 7.1.1
python-dateutil 2.8.2
python-gitlab 2.10.1
pytz 2018.5
pytz 2021.3
pytz 2022.1
pywin32-ctypes 0.1.2
pywin32 223
queuelib 1.5.0
requests-toolbelt 0.9.1
requests 2.19.1
requests 2.25.1
requests 2.29.0
ruamel-yaml-conda 0.15.100
service-identity 17.0.0
setuptools 40.2.0
setuptools 44.1.1
setuptools 59.6.0
setuptools 61.2.0
setuptools 67.7.2
setuptools 67.8.0
simplejson 3.17.6
six 1.11.0
six 1.16.0
tempora 1.13
tomli 1.2.2
tox 3.2.1
tox 3.2.2.dev2 g37e2b53
tqdm 4.57.0
traceback2 1.4.0
twilio 6.16.1
unittest2 1.1.0
urllib3 1.23
urllib3 1.26.15
urllib3 1.26.5
vcrpy 4.0.2
virtualenv 16.0.0
w3lib 1.19.0
webencodings 0.5.1
wheel 0.31.1
wheel 0.37.1
wheel 0.40.0
wrapt 1.13.3
wsgiref 0.1.2
xopen 1.7.0
zipp 1.0.0
zope.interface 4.5.0
zstandard 0.19.0