# Packages column of https://docs.google.com/spreadsheets/d/1tApLhVqxRZ2VOuMH_aPUgFENQJfbLlB_PFH_Ah_q7hM/edit?ts=5eb957ba#gid=543782716
## resolved: "20 dependencies on R packages for pigx-rnaseq would need to go here"
## todo: 20 dependencies on R packages for pigx-scrnaseq would need to go here
## Fixme: pigx-rnaseq and pigx-scrnaseq are missing in this list


nextflow
snakemake
nf-core
abacas
allelecount
ascat
bcftools
bedtools
biopython
ncbi-blast+
bowtie2
busco
bustools
bwa
cat
centrifuge
changeo
cutadapt
diamond
deeptools
drop-seq-tools
fastp
fastqc
filtlong
freebayes
gatk
graphmap2
guppy
htslib
htseq
ivar
java
kallisto
kraken2
krona
lumpy
manta
megahit
metabat
minia
minimap2
multiqc
muscle
nanolyse
nanoplot
numpy
pandas
parallel-fastq-dump
picard
porechop
presto
prodigal
pycoqc
python
qcat
qualimap
quast
r-cran-alakazam
r-cran-ggplot2
r-cran-rmarkdown
r-cran-shazam
r-cran-tigger
r-cran-locfit
r-bioc-deseq2
r-bioc-tximport
r-cran-data.table
r-cran-rlang
r-cran-ggrepel
r-cran-dt
r-cran-pheatmap
r-cran-corrplot
r-cran-reshape2
r-cran-plotly
r-cran-scales
r-cran-crosstalk
r-cran-gprofiler
r-bioc-summarizedexperiment
r-bioc-rtracklayer
r-cran-rjson
salmon
samtools
snpeff
snpsift
spades
sra-toolkit
rna-star
strelka
tiddit
trim-galore
unicycler
varscan2
vcftools
vep
vg
