Restricting search to CURRENT branch. (
wip/salmon | | Transcript-level quantification of RNA-seq from lightweight alignments |
wip/bwa | | Map low-divergent sequences against a large reference genome |
wip/libbacon | | Miscellaneous experimental functions |
wip/ape | | Another Programmers Editor |
wip/pbcopper | | Core C++ library for data structures, algorithms, and utilities |
biology/trimmomatic | | Flexible read trimming tool for Illumina NGS data |
wip/ganglia-webfrontend | | PHP based frontend for the Ganglia Cluster Monitor |
wip/gtextutils | | Gordon text utilities |
wip/meep-openmpi | | FDTD simulation software to model electromagnetic systems |
wip/fastahack | | Utilities for indexing and sequence extraction from FASTA files |
wip/parafly | | Process the commands in parallel on a single server |
wip/metal | | Meta-analysis of genomewide association scans |
wip/py-ufl | | Unified Form Language for finite element discretizations |
wip/pbbam | | PacBio BAM C++ library, with SWIG bindings |
wip/vcftools | | Tools for working with VCF genomics files |
wip/suitesparse | | SuiteSparse is a set of packages for sparse matrices calculation |
wip/ddocent | | Bash pipeline for RAD sequencing |
wip/mpb | | MIT Photonic Bands |
wip/yaggo | | Generate command line parser using getopt_long |
wip/daligner | | Find all significant local alignments between reads |
wip/dlpoly-classic | | General purpose classical molecular dynamics |
wip/py-rdflib340 | | Python library for RDF manipulation |
wip/rsem | | RNA-Seq by Expectation-Maximization |
wip/samtools | | Tools for manipulating sequence alignment maps |
wip/man2html | | Convert nroff(1) man pages to HTML |
wip/htslib | | C library for high-throughput sequencing data formats |
biology/plinkseq | | C/C++ library for working with human genetic variation data |
wip/cluster-admin | | HPC cluster admin tools |
biology/plink | | Whole-genome association analysis toolset |
wip/bolt-lmm | | Statistics for testing association between phenotype and genotypes |
wip/py-viper | | Scientific plotter and run-time visualization module |
wip/pear | | Memory-efficient and highly accurate pair-end read merger |
wip/py-macs2 | | Novel algorithm for identifying transcript factor binding sites |
wip/p5-trimgalore | | Wrapper around Cutadapt and FastQC for adapter and quality trimming |
wip/fbsd2pkg | | Convert a FreeBSD port framework to a pkgsrc package |
biology/bwa | | Map low-divergent sequences against a large reference genome |
wip/denyhosts | | Block hosts with too many failed login attempts |
wip/vcflib | | C++ library and CLI tools for parsing and manipulating VCF files |
biology/cdhit | | Clustering and comparing protein or nucleotide sequences |
wip/fftw-openmpi | | Collection of fast C routines to compute DFTs |
wip/openmx-openmpi | | Nano-scale material simulations based on DFT |
wip/dazz_db | | Dresden assembler for long read DNA projects |
wip/gmap | | Genomic Mapping and Alignment Program for mRNA and EST Sequences |
wip/fastaunique | | Sort and uniq fasta files |
wip/py-pbfalcon | | Experimental PacBio diploid assembler |
wip/p5-IPC-Open3-Simple | | Simple alternative to IPC::Open3 |
wip/linux-ukbgene | | Tool for accessing UK Biobank data |
wip/haplohseq | | Identify regions of allelic imbalance |
wip/blasr_libcpp | | Library for analyzing PacBio sequences |
wip/tophat | | Fast splice junction mapper for RNA-Seq reads |
wip/py-rdfextras | | Collection of packages providing extras based on RDFLib 3 |
wip/lmod | | Dynamic modification of a users environment |
wip/spcm | | Simple, portable cluster management |
wip/detab | | Replace tabs with spaces in a text file |
wip/hisat2 | | Alignment program for mapping next-generation sequencing reads |
wip/blasr | | PacBio(R) long read aligner |
wip/ad2vcf | | Add allelic depth info from a SAM stream to a VCF file |
wip/twintk | | Terminal Windows Toolkit |
wip/libpare | | Pointer Array Regular Expressions |
wip/py-anvio | | Analysis and visualization platform for omics data |
wip/libzeep | | Make it easy to create SOAP servers |
wip/py-biopython | | Collection of Python modules for bioinformatics |
wip/xssp | | Software for creating DSSP and HSSP files |
wip/py-pysam | | Python module for reading, manipulating and writing genomic data sets |
wip/R-optparse | | Command Line Option Parser |
wip/vcf-split | | Split a multi-sample VCF into single-sample VCFs |
wip/famsa | | Algorithm for large-scale multiple sequence alignments |
wip/py-ete3 | | Python Environment for (phylogenetic) Tree Exploration |
wip/py-snakemake | | Reduce the complexity of creating workflows |
wip/py-eggnog-mapper | | Fast functional annotation of novel DNA or protein sequences |
wip/optibench | | Benchmark to measure optimal sustained memory and disk performance |
wip/pkg-dev | | Scripts to automate common tasks in pkgsrc development |
wip/R-getopt | | C-Like getopt Behavior |
wip/fasttree | | Approximately-maximum-likelihood phylogenetic trees from alignments |
textproc/man2html | | Convert nroff(1) man pages to HTML |
wip/py-htseq | | Framework to analyze data from high-throughput sequencing assays |
wip/ncbi-blast+ | | NCBI implementation of Basic Local Alignment Search Tool |
wip/meep | | FDTD simulation software to model electromagnetic systems |
wip/antlr | | ANother Tool for Language Recognition |
wip/udunits2 | | Library for manipulating units of physical quantities |
wip/plink | | Whole genome association analysis toolset |
wip/seqtk | | Tool for processing sequences in FASTA/FASTQ format |
wip/fftw-mpich | | Collection of fast C routines to compute DFTs |
math/udunits | | Library and program for manipulating units of physical quantities |
wip/filevercmp | | Filevercmp function as in sort --version-sort |
wip/fsom | | Tiny C library for managing SOM (Self-Organizing Maps) neural networks |
wip/slclust | | Single-linkage clustering with Jaccard similarity |
biology/hisat2 | | Alignment program for mapping next-generation sequencing reads |
wip/bpcscripts | | Gast Illumina processing |
archivers/libaec | | Adaptive entropy coding library |
wip/runas | | Wrapper around su for running a command as another user |
wip/intervaltree | | Minimal C++ interval tree implementation |
wip/unanimity | | Consensus library and applications |
wip/kallisto | | Quantify abundances of transcripts from RNA-Seq data |
wip/structure | | Multi-locus genotype data to investigate population structure |
wip/jellyfish | | Fast, memory-efficient counting of k-mers in DNA |
wip/R-mpfr | | Multiple Precision Floating Point Arithmetic for R |
wip/fastp | | Ultra-fast all-in-one FASTQ preprocessor |
wip/mcl | | Fast and scalable unsupervised cluster algorithm for graphs |
wip/webbrowser | | Proxy script for launching best available web browser |
wip/tabixpp | | C++ wrapper to tabix indexer |
wip/bcftools | | Tools for manipulating BCF and VCF variant call files |
wip/gromacs | | Molecular dynamics package |
wip/wgrib2 | | Tools for managing GRIB weather data files |
biology/ncbi-blast+ | | NCBI implementation of Basic Local Alignment Search Tool |
wip/canu | | Single molecule sequence assembler for genomes large and small |
wip/singularity | | Application container for Linux |
wip/py-graph-tool | | Python module for manipulation and statistical analysis of graphs |
wip/cereal | | C++11 library for serialization |
wip/mpb-openmpi | | MIT Photonic Bands |
wip/numactl | | Non Uniform Memory Access tools |
wip/centrifuge | | Novel microbial classification engine |
wip/multichoose | | Generate multiset combinations (n multichoose k) |
biology/kallisto | | Quantify abundances of transcripts from RNA-Seq data |
biology/samtools | | Tools for manipulating sequence alignment maps |
wip/muscle | | MUltiple Sequence Comparison by Log-Expectation |
biology/stacks | | Software pipeline for building loci from short-read sequences |
biology/bcftools | | Tools for manipulating BCF and VCF variant call files |
security/munge | | Authentication service for creating and validating credentials |
biology/canu | | Single molecule sequence assembler for genomes large and small |
biology/vsearch | | Versatile open-source tool for metagenomics |
wip/openmpi | | Open source implementation |
wip/jellyfish2 | | Fast, memory-efficient counting of k-mers in DNA |
biology/py-dnaio | | Read and write FASTQ and FASTA files |
wip/p5-transdecoder | | Identify candidate coding regions within transcript sequences |
biology/py-cutadapt | | Find and remove adapter sequences, primers, poly-A tails, etc |
devel/libctl | | Guile-based flexible control file library for scientific simulations |
wip/auto-admin | | Portable tools for automating systems management |
parallel/slurm-wlm | | Simple Linux Utility for Resource Management |
wip/linux-gcta | | Tool for Genome-wide Complex Trait Analysis |
wip/slurm-wlm | | Simple Linux Utility for Resource Management |
wip/packmol | | Pack molecules in defined regions of space |
wip/biolibc | | Low-level high-performance bioinformatics library |
textproc/R-data.table | | Extension of data.frame |
textproc/R-cellranger | | Translate spreadsheet cell ranges to rows and columns |
wip/pbseqan | | PacBio patched and stripped down seqan |
wip/armadillo | | C++ linear algebra library |
wip/epacts | | Efficient and Parallelizable Association Container Toolbox |
wip/py-fiat | | Finite element Automatic Tabulator |
wip/meep-mpi | | FDTD simulation software to model electromagnetic systems |
wip/cdbfasta | | Fast indexing and retrieval of fasta records from flat file databases |
wip/basic-stats | | Command-line tool to perform basic statistics on tabular data |
wip/vsearch | | Versatile open-source tool for metagenomics |
wip/py-hostlist | | Manage SLURM host lists |
wip/cdhit | | Clustering and comparing protein or nucleotide sequences |
wip/plink2 | | Whole genome association analysis toolset |
wip/gemma | | Genome-wide Efficient Mixed Model Association |
wip/hmmer | | Profile hidden Markov models for biological sequence analysis |
wip/vcf2hap | | Generate .hap file from VCF for haplohseq |
wip/ufc | | Unified framework for finite element assembly |
wip/py-ffc | | C++ code generator for multilinear forms |
wip/smithwaterman | | Smith-waterman-gotoh alignment algorithm |
wip/py-cutadapt | | Find and remove adapter sequences, primers, poly-A tails, etc |
devel/swig2 | | Simplified Wrapper and Interface Generator (version 2) |
wip/prodigal | | Prokaryotic Dynamic Programming Genefinding Algorithm |
wip/fastx-toolkit | | CLI tools for Short-Reads FASTA/FASTQ files preprocessing |
wip/igv | | Visualization tool for genomic datasets |
biology/igv | | Visualization tool for genomic datasets |
wip/fastool | | Simple and quick FastQ and FastA tool for file reading and conversion |
wip/gromacs2018 | | Molecular dynamics package |
wip/munge | | Authentication service for creating and validating credentials |
biology/fastp | | Ultra-fast all-in-one FASTQ preprocessor |
wip/trinity | | Assembles transcript sequences from Illumina RNA-Seq data |
wip/rainbow | | Short reads clustering and local assembly |
biology/htslib | | C library for high-throughput sequencing data formats |
wip/py-dnaio | | Read and write FASTQ and FASTA files |
devel/R-rematch | | Match regular expressions with a nicer API |
wip/py-pypeflow | | Lightweight and reusable make/flow data process library |
wip/libaec | | Adaptive entropy coding library |
wip/fvcom2 | | Prognostic coastal ocean circulation model |
wip/tbb | | Library that provides thread building blocks |
parallel/ganglia-monitor-core | | Ganglia cluster monitor, monitoring daemon |
wip/docviewer | | Generic command to automatically select a document viewer |
wip/bowtie | | Ultrafast, memory-efficient short read aligner |
wip/wip-tools | | Tools for developing wip packages |
biology/fastqc | | Quality control tool for high throughput sequence data |
wip/bowtie2 | | Ultrafast, memory-efficient short read aligner |
wip/slurm-wlm-devel | | Simple Linux Utility for Resource Management |
wip/pooler | | Optimise DNA sequencing primer-set combinations |
sysutils/auto-admin | | Portable tools for automating systems management |
biology/bowtie2 | | Ultrafast, memory-efficient short read aligner |
devel/py-xopen | | Open compressed files transparently |
biology/bedtools | | Swiss army knife for genome arithmetic |
wip/bedtools | | Swiss army knife for genome arithmetic |