KING
- Ebuilds: 1, Testing: 2.2.7 Description: Check family relationship and infer population structure
Homepage:https://kingrelatedness.com License: all-rights-reserved
SPAdes
- Ebuilds: 1, Testing: 3.15.5 Description:
truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
dipspades is assembly module for highly polymorphic diploid genomes
Homepage:https://cab.spbu.ru/software/spades License: GPL-2
YASRA
- Ebuilds: 1, Testing: 2.33 Description: Yet Another Short Read Assembler aligning to a reference using LASTZ
Homepage:http://www.bx.psu.edu/miller_lab/ License: GPL-2
abacas
- Ebuilds: 1, Testing: 1.3.1 Description: Order and orientate DNA contigs even via 6-frame protein alignments
Homepage:https://abacas.sourceforge.net License: GPL-2+
afni
- Ebuilds: 3, Testing: 24.1.16 Description:
Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying
functional MRI data—a technique for mapping human brain activity.
Homepage:https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/ License: GPL-3+
aghermann
- Ebuilds: 1, Testing: 1.1.2-r2 Description:
Aghermann is a program designed around a common workflow in
sleep-research, complete with scoring facility; cairo subpixel
drawing on screen or to file; conventional PSD and EEG Micrcontinuity
profiles; Independent Component Analysis; artifact detection; and
Process S simulation following Achermann et al, 1993.
Homepage:http://johnhommer.com/academic/code/aghermann License: GPL-2+
ants
- Ebuilds: 1, Testing: 2.4.3 Description:
ANTs extracts information from complex datasets that include imaging
(Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing,
interpreting and visualizing multidimensional data. ANTs is popularly
considered a state-of-the-art medical image registration and segmentation
toolkit. ANTsR is an emerging tool supporting standardized multimodality
image analysis. ANTs depends on the Insight ToolKit (ITK), a widely used
medical image processing library to which ANTs developers contribute.
Homepage:https://stnava.github.io/ANTs/ License: BSD
bambus
- Ebuilds: 1, Testing: 2.33-r2 Description: Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.
Homepage:
https://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS
https://sourceforge.net/projects/amos/files/bambus License: Artistic
biobambam2
- Ebuilds: 2, Testing: 2.0.146 Description:
This package contains some tools for processing BAM files including
bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
bamsort: reads BAM and writes BAM resorted by coordinates or query name
bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name
Homepage:https://gitlab.com/german.tischler/biobambam2
https://github.com/gt1/biobambam2 License: GPL-3 MIT
bismark
- Ebuilds: 1, Testing: 0.23.0 Description:
Bismark is a program to map bisulfite treated sequencing reads to a genome of
interest and perform methylation calls in a single step. The output can be
easily imported into a genome viewer, such as SeqMonk, and enables a researcher
to analyse the methylation levels of their samples straight away. It's main
features are: (1) Bisulfite mapping and methylation calling in one single step;
(2) Supports single-end and paired-end read alignments; (3) Supports ungapped
and gapped alignments; (4) Alignment seed length, number of mismatches etc. are
adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG
and CHH context.
Homepage:https://www.bioinformatics.babraham.ac.uk/projects/ License: GPL-3+
brat_bw
- Ebuilds: 1, Testing: 2.0.1 Description: Bisulfite-aware short read mapper, FM-index, no InDel support
Homepage:http://compbio.cs.ucr.edu/brat/ License: GPL-3
brat_nova
- Ebuilds: 1, Testing: 20160103 Description: Bisulfite-aware short read mapper, FM-index, accepts 1 InDel/read, local align
Homepage:http://compbio.cs.ucr.edu/brat/ License: GPL-3
brkraw
- Ebuilds: 1, Testing: 0.3.11 Description: Fast and easy statistical learning on NeuroImaging data
Homepage:https://github.com/BrkRaw/brkraw License: GPL-3
bru2nii
- Ebuilds: 1, Testing: 1.0.20180303 Description:
This is a simple tool for converting Bruker ParaVision MRI data to
the NIfTI file format. It includes both a drag-and-drop graphical
interface (Bru2Nii) as well as a command line tool (Bru2).
Homepage:https://github.com/neurolabusc/Bru2Nii License: || ( Artistic GPL-1+ )
bruker2nifti
- Ebuilds: 1, Testing: 1.0.4-r1 Description:
Bruker2nifti is an open source medical image format converter from
raw Bruker ParaVision to NifTi, without any intermediate step through
the DICOM standard format.
Homepage:https://github.com/SebastianoF/bruker2nifti License: MIT
cnrun
- Ebuilds: 1, Testing: 2.1.0-r2 Description:
CNrun is a neuronal network simulator, with these features:
* a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and
Alpha-Beta synapses;
* a 6-5 Runge-Kutta integration method: slow but precise, adjustable;
* Poisson, Van der Pol, Colpitts oscillators and interface for
external stimulation sources;
* NeuroML network topology import/export;
* logging state variables, spikes;
* implemented as a Lua module, for scripting model behaviour (e.g.,
to enable plastic processes regulated by model state);
* interaction (topology push/pull, async connections) with other
cnrun models running elsewhere on a network, with interactions
(planned).
Note that there is no `cnrun' executable, which existed in cnrun-1.*.
Instead, you write a script for your simulation in Lua, and execute
it as detailed in /usr/share/lua-cnrun/examples/example1.lua.
Homepage:http://johnhommer.com/academic/code/cnrun License: GPL-2+
codonw
- Ebuilds: 1, Testing: 1.4.4-r2 Description: Multivariate statistical analysis of codon and amino acid usage
Homepage:https://codonw.sourceforge.net/ License: GPL-2
cutadapt
- Ebuilds: 1, Testing: 4.9 Description: Adapter trimming and other preprocessing of high-throughput sequencing reads
Homepage:https://github.com/marcelm/cutadapt/ License: MIT
dargcc_bidsdata
- Ebuilds: 1, Testing: 1.0 Description:
BIDS data selection encompassing the wildtype mouse group form the
"Dysfunctional Autism Risk Genes Cause Circuit-Specific Connectivity
Deficits With Distinct Developmental Trajectories" publication, with
DOI: 10.1093/cercor/bhy046 .
Homepage:https://academic.oup.com/cercor/article/28/7/2495/4975475 License: GPL-3
dcm2niix
- Ebuilds: 1, Testing: 1.0.20210317 Description:
dcm2niix is a designed to convert neuroimaging data from the DICOM
format to the NIfTI format. ICOM provides many ways to store/compress
image data, known as transfer syntaxes.
Homepage:https://github.com/rordenlab/dcm2niix License: BSD
dipy
- Ebuilds: 1, Testing: 1.1.1-r1 Description:
Dipy is a free and open source software project for computational neuroanatomy, focusing mainly on
diffusion magnetic resonance imaging (dMRI) analysis. It implements a broad range of algorithms for
denoising, registration, reconstruction, tracking, clustering, visualization, and statistical
analysis of MRI data.
Homepage:https://github.com/nipy/dipy License: BSD
drlfom_bidsdata
- Ebuilds: 1, Testing: 1.1 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the DRLFOM publication. The data represents
optp-fMRI mouse brain scans with CBV contrast, tracking serotonergic
stimulation over the course of a fluoxetine drinking water treatment.
Homepage:https://chymera.eu/docs/focus/open-science/ License: CC-BY-SA-4.0
edena
- Ebuilds: 1, Testing: 3.131028 Description: De novo short read OLC assembler (overlap-layout-consensus)
Homepage:http://www.genomic.ch/edena.php License: GPL-3
freebayes
- Ebuilds: 1, Testing: 1.3.5 Description: Bayesian gen. variant detector to find short polymorphisms
Homepage:https://github.com/ekg/freebayes License: MIT
grappa
- Ebuilds: 1, Testing: 2.0 Description: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms
Homepage:https://www.cs.unm.edu/~moret/GRAPPA/ License: GPL-2
hexamer
- Ebuilds: 1, Testing: 19990330 Description: Predict CDS using 6mers without deriving information from base composition
Homepage:http://www.sanger.ac.uk/resources/software License: all-rights-reserved
irsabi_bidsdata
- Ebuilds: 1, Testing: 1.4 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the IRSABI publication. The data represents
f/MRI mouse brain scans with both BOLD and CBV contrasts, and acquired
during optogenetic stimulation over multiple sessions including acute
(i.v.) and chronic (s.c.) fluoxetine administration sessions.
Homepage:https://chymera.eu/docs/focus/open-science/ License: CC-BY-SA-4.0
lastz
- Ebuilds: 1, Testing: 1.04.03 Description: A pairwise DNA sequence aligner, a BLASTZ replacement
Homepage:http://www.bx.psu.edu/~rsharris/lastz/ License: all-rights-reserved
lemur-brain-atlas
- Ebuilds: 1, Testing: 0.1 Description:
MRI template and 120-region atlas for the mouse lemur primate Microcebus
murinus. Generated from 34 animals aged 15-58 months old scanned at 7T
using a T2-weighted sequence, resolution 115 × 115 × 230 µm. The template
was up-sampled to 91 µm isotropic for hand-segmentation of structures,
and also used to create probability maps of grey matter, white matter and
cerebro-spinal fluid.
Homepage:https://www.nitrc.org/projects/mouselemuratlas License: CeCILL-2
mmseqs2
- Ebuilds: 1, Testing: 13.0-r1 Description:
MMseqs2 (Many-against-Many sequence searching) is a software suite toi
search and cluster huge protein and nucleotide sequence sets.
MMseqs2 is open source GPL-licensed software implemented in C++.
The software is designed to run on multiple cores and servers
and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the
same sensitivity. It can perform profile searches with the same
sensitivity as PSI-BLAST at over 400 times its speed.
Homepage:https://github.com/soedinglab/MMseqs2 License: GPL-3
msautil
- Ebuilds: 1, Testing: 1.1-r1 Description: Reformat/edit FASTA files and compute simple statistics (N50, quartiles, mode)
Homepage:http://bioresearch.byu.edu/msa License: all-rights-reserved
multiqc
- Ebuilds: 1, Testing: 1.33 Description: Aggregate bioinformatics results across many samples into a single report
Homepage:https://multiqc.info/ License: GPL-3
nilearn
- Ebuilds: 1, Testing: 0.9.1-r1 Description:
Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
It leverages the scikit-learn Python toolbox for multivariate statistics with applications
such as predictive modelling, classification, decoding, or connectivity analysis.
Homepage:http://nilearn.github.io/ License: BSD
nitime
- Ebuilds: 2, Testing: 0.10.2 Description:
Nitime is a library for time-series analysis of data from neuroscience experiments
in both the time and spectral domains.
Homepage:http://nipy.org/nitime/index.html License: BSD
ntCard
- Ebuilds: 2, Testing: 1.2.2 Description: Estimate k-mer coverage histogram of genomics data
Homepage:https://github.com/bcgsc/ntCard License: MIT
nxtrim
- Ebuilds: 1, Testing: 0.4.3 Description: Trim Illumina TruSeq adapters and split reads by Nextera MatePair linker
Homepage:https://github.com/sequencing/NxTrim License: BSD-2
open-ephys-gui
- Ebuilds: 3, Testing: 99999999 Description: Processing, recording, and visualizing multichannel ephys data
Homepage:https://open-ephys.org/gui/ License: GPL-3
opfvta_bidsdata
- Ebuilds: 1, Testing: 2.0 Description:
BIDS-formatted MRI data recorded at the ETH/UZH Animal Imaging Center
and first associated with the OPFVTA publication. The data represents
f/MRI mouse brain scans with both BOLD and CBV contrasts, using block
and phasic stimulation protocols delivered via a laser to the VTA,
which is rendered sensitive by channelrhodopsin expression under
the dopamine transporter promoter.
Homepage:http://chymera.eu/docs/focus/open-science/ License: CC-BY-SA-4.0
prinseq-lite
- Ebuilds: 1, Testing: 0.20.4 Description: Describe, trim, reformat and convert to or form FASTA/FASTQ files
Homepage:http://prinseq.sourceforge.net/ License: GPL-3+
proda
- Ebuilds: 1, Testing: 1.0 Description: Multiple alignment of protein sequences with repeated and shuffled elements
Homepage:http://proda.stanford.edu/ License: public-domain
quicktree
- Ebuilds: 1, Testing: 2.5 Description: Rapid reconstruction of phylogenies by the Neighbor-Joining method
Homepage:https://github.com/khowe/quicktree/ License: Apache-2.0
rat-brain-templates
- Ebuilds: 1, Testing: 0.2 Description:
Digital rat brain template collection containing data files in NIfTI
format oriented in the standard RAS space, with origin at bregma for
use in magnetic resonance rat brain imaging.
Homepage:https://gitlab.com/FOS-FMI/rat-brain-templates_generator License: fairuse
samri
- Ebuilds: 3, Testing: 9999 Description:
SAMRI provides fMRI preprocessing, metadata parsing, and data analysis functions
and pipelines. SAMRI integrates functionalities from a number of other packages
to create higher-level tools.
Homepage:https://github.com/IBT-FMI/SAMRI
snapgene
- Ebuilds: 2, Testing: 8.2.2 Description: Software for plasmid mapping, primer design, and restriction site analysis
Homepage:https://www.snapgene.com/snapgene-viewer License: snapgene
spm
- Ebuilds: 1, Testing: 12_p7771 Description: Analysis of brain imaging data sequences for Octave or Matlab
Homepage:https://www.fil.ion.ucl.ac.uk/spm/ License: GPL-2+