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Jason W. Bacon e44f917e29 biology/erminej: Analyses of gene sets, e.g. gene expression profiling 
ErmineJ performs analyses of gene sets in high-throughput genomics data
such as gene expression profiling studies. A typical goal is to
determine whether particular biological pathways are "doing something
interesting" in an experiment that generates long lists of candidates.
The software is designed to be used by biologists with little or no
informatics background (but if you do, you might be interested in the
CLI or the R support).
2021-07-09 07:26:58 -05:00
..
abyss biology/abyss: Update 2.3.0-3 -> 2.3.1 2021-04-22 10:18:02 -07:00
ad2vcf biology/ad2vcf: Remove comment used to silence portlint 2021-06-11 10:39:02 -05:00
artemis Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
avida Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
babel all: Remove all other $FreeBSD keywords. 2021-04-06 16:31:13 +02:00
bamtools biology/bamtools: Update to 2.5.2 2021-07-06 13:10:54 -05:00
bbmap biology/bbmap: BBMap short read aligner, and other bioinformatic tools 2021-04-18 11:21:29 -05:00
bcftools math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
bedtools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bioawk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biococoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biolibc biology/biolibc: Remove comment used to silence portlint 2021-06-11 10:38:27 -05:00
bioparser One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biosoup One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biostar-tools biology/biostar-tools: Add biology/py-goatools to metaport depends 2021-07-02 12:03:10 -05:00
bolt-lmm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie2 biology/bowtie2: Update to 2.4.4 2021-05-24 11:35:43 -05:00
bwa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
canu One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cd-hit biology/cd-hit: fix build on powerpc 2021-06-10 00:35:36 +00:00
cdbfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
checkm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
clustal-omega One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
clustalw Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
cufflinks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cytoscape biology/cytoscape: mark unconditionally BROKEN 2021-05-12 14:55:52 +03:00
ddocent One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
diamond biology/diamond: Update to 2.0.11-1 2021-07-06 10:15:24 -03:00
dsr-pdb One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
edlib One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
emboss Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
erminej biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00
exonerate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fasta Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
fasta3 Deorbit RESTRICTED && NO_CDROM, part one. 2021-05-06 13:47:41 +02:00
fastahack One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastdnaml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fastool One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastp One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastqc One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fasttree biology/fasttree: fix build on armv7 2021-06-15 08:41:19 +00:00
fastx-toolkit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
figtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fluctuate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
freebayes One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
garlic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gatk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gcta One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gemma math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
generand One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gff2ps Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gmap Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gperiodic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
graphlan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
groopm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
haplohseq One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hhsuite biology/hhsuite: fix build on powerpc64* 2021-07-08 13:13:54 +00:00
hisat2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hmmer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
htslib Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
hyphy biology/hyphy: Update to 2.5.31 2021-06-05 20:00:24 -03:00
igv biology/igv: Fix build 2021-06-27 05:33:51 -04:00
infernal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
iolib biology/iolib: Drop maintainership 2021-05-19 20:56:24 +01:00
iqtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
jalview biology/jalview: Fix build 2021-06-27 05:30:39 -04:00
jellyfish One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
kallisto One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
lamarc Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
libbigwig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libgtextutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libsbml biology/libsbml: Rename LIBXML option to LIBXML2 2021-05-12 05:46:56 +08:00
linux-foldingathome biology/linux-foldingathome: Update to 7.6.21 2021-06-25 19:13:19 +02:00
mafft Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mapm3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
migrate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
minimap2 biology/minimap2: Update to 2.20 2021-05-29 16:06:34 -05:00
mmseqs2 biology/mmseqs2: Fix runtime error when built with clang 2021-06-29 09:04:48 -05:00
molden graphics/mesa-libs: Bump reverse deps for libglvnd 2021-06-22 11:53:08 -07:00
mopac Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mothur biology/mothur: Update 1.45.2 -> 1.45.3 2021-05-09 09:11:11 -07:00
mrbayes *: Remove unnecessary 'port' argument from USES=readline 2021-05-15 09:14:04 +02:00
mummer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
muscle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-blast+ biology/ncbi-blast+: Update to 2.12.0 2021-07-02 11:48:20 -05:00
ncbi-cxx-toolkit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
ncbi-entrez-direct biology/ncbi-entrez-direct: Update to 14.9.20210423_1 2021-04-26 11:53:11 -05:00
ncbi-toolkit Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-vdb devel/libepoll-shim: update to 0.0.20210418 2021-04-26 14:17:32 +00:00
ngs-sdk biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH 2021-04-15 10:01:31 -07:00
p5-AcePerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-ASN1-EntrezGene Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Cluster Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Coordinate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das-Lite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-EMBL Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-NCBIHelper biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7 2021-07-06 22:56:10 +08:00
p5-Bio-FeatureIO Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-GFF3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Glite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Graphics Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-MAGETAB Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-NEXUS Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Phylo Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-SCF Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Variation Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl-Run Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-transdecoder One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
p5-TrimGalore One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
paml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
pbbam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pbseqan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
peak-classifier biology/peak-classifier: Classify peaks based on GFF features 2021-06-14 11:40:33 -05:00
pear-merger One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
phrap Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phred Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phyml Clean up some things 2021-04-15 10:31:56 +02:00
picard-tools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
plink One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pooler One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
primer3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
prodigal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
prodigy-lig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
protomol Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
psi88 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bigwig biology/py-bigwig: Fix packaging with Python 3.8+ 2021-04-21 09:41:29 +02:00
py-biom-format One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-biopython Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bx-python Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-crossmap biology/py-crossmap: Update to 0.5.4 2021-04-21 08:31:13 -05:00
py-cutadapt biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 08:20:39 -05:00
py-dnaio biology/py-dnaio: Update to 0.5.1 2021-05-04 08:19:25 -05:00
py-ete3 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-gffutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-goatools biology/py-goatools: Tools for processing and visualizing Gene Ontology terms 2021-07-02 12:00:29 -05:00
py-gtfparse One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-hits One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-loompy One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-macs2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-multiqc math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1 2021-04-27 01:56:19 -07:00
py-orange3-single-cell One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pandas-charm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pyfaidx biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5 2021-04-23 14:57:50 -07:00
py-pysam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-resdk biology/py-resdk: Update 13.2.0 -> 13.3.0 2021-05-24 00:26:50 -07:00
py-scikit-bio One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-xenaPython One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pyfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
python-nexus Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rainbow One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
rampler One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
readseq biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint 2021-04-18 09:20:28 -05:00
recombine Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ruby-bio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio biology/rubygem-bio: Update to 2.0.2 2021-07-01 04:44:06 +08:00
rubygem-bio-executables Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-old-biofetch-emulator Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-shell Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
samtools Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
scrm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
seaview Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan1 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan3 biology/seqan3: Update 3.0.2-1195 -> 3.0.3 2021-05-29 22:38:08 -07:00
seqan-apps biology/seqan-apps: fix packaging on armv7 2021-06-21 08:11:25 +00:00
seqio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqkit biology/seqkit: Update 0.16.0 -> 0.16.1 2021-05-19 23:02:26 -07:00
seqtk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sim4 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
slclust One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
smithwaterman One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
snpeff biology/snpeff: Improvements to Makefile and patches 2021-04-19 11:41:58 -05:00
spoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sra-tools biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives 2021-06-22 12:55:15 -05:00
stacks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
star One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
stringtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
subread One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
tabixpp One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
taxonkit biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit 2021-05-26 15:25:22 -07:00
treekin math/lapack: +math/blas et al., upgrade to 3.9.1 2021-06-13 19:48:12 +02:00
treepuzzle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
trimadap One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
trimmomatic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
tRNAscan-SE Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ucsc-userapps biology/ucsc-userapps: Update to v414 2021-05-15 10:23:08 -05:00
ugene biology/ugene: update Unipro UGENE to version 39.0. 2021-06-25 17:56:47 +00:00
unikmer biology/unikmer: Update 0.18.0 -> 0.18.1 2021-06-24 15:06:35 -07:00
vcf2hap biology/vcf2hap: Remove comment used to silence portlint 2021-06-11 10:40:11 -05:00
vcf-split biology/vcf-split: Update to 0.1.2 2021-06-11 10:05:19 -05:00
vcflib One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vcftools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
velvet Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
viennarna math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
vsearch biology/vsearch: Update to 2.17.1 2021-06-19 07:33:58 -05:00
vt One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
wise Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Makefile biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00