Section 1 of the manual describes user commands and tools, for example, file manipulation tools, shells, compilers, web browsers, file and image viewers and editors, and so on.
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- NAST-iEr
- nast-ier - NAST-based DNA alignment tool
- NCLconverter
- report of content of NEXUS file
- NDist
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- NEXUSnormalizer
- rewrites NEXUS file to standard out with consistent indentation and syntax
- NEXUSvalidator
- validate NEXUS file
- NF
- col1 .. col9, NF - awk and print a column (based on the name of the program, 1-9)
- NIfTI1ToDicom
- Read a NIfTI-1 image input format files and create an image of a specified or appropriate SOP Class
- NPlam
- NetPIPE - Net work
- NPlam2
- NetPIPE - Net work
- NPmpich2
- NetPIPE - Net work
- NPopenmpi
- NetPIPE - Net work
- NPopenmpi2
- NetPIPE - Net work
- NPpvm
- NetPIPE - Net work
- NPtcp
- NetPIPE - Net work
- NRRDToDicom
- Read an NRRD image input format files and create an image of a specified or appropriate SOP Class
- NRswitchg
- For each v, complement the edges from N(v) to V(G)-N(v)-v
- NSBrowserTest
- gnustep-examples - various example GNUstep tools/applications
- NSImageTest
- gnustep-examples - various example GNUstep tools/applications
- NSPanelTest
- gnustep-examples - various example GNUstep tools/applications
- NSScreenTest
- gnustep-examples - various example GNUstep tools/applications
- NanoFilt
- filtering and trimming of long read sequencing data
- NanoLyse
- remove lambda phage reads from a fastq file
- NanoSV
- structural variant caller for the Nanopore
- NanoStat
- manual page for NanoStat 1.4.0
- NitrokeyAuthenticator
- TOTP authenticator application for Nitrokey Pro2 and LibremKey
- NoiseFilterGaussian
- topp - library for LC/MS data management and analysis - tools
- NoiseFilterSGolay
- topp - library for LC/MS data management and analysis - tools
- NovorAdapter
- topp - library for LC/MS data management and analysis - tools
- NucleicAcidSearchEngine
- topp - library for LC/MS data management and analysis - tools
- OMSSAAdapter
- topp - library for LC/MS data management and analysis - tools
- ONE2LA
- daligner - local alignment discovery between long nucleotide sequencing reads
- OSCAR
- Open Source CPAP Analysis Reporter
- OgreMeshUpgrader
- OgreMeshUpgrade - upgrades .mesh files to the latest version
- OgreXMLConverter
- converts data between XML and Ogre binary formats
- OpenBoard
- cross-platform Interactive White-Board Application
- OpenJazz
- Jack Jazzrabbit 1 game engine reimplementation
- OpenMSInfo
- topp - library for LC/MS data management and analysis - tools
- OpenPepXL
- topp - library for LC/MS data management and analysis - tools
- OpenPepXLLF
- topp - library for LC/MS data management and analysis - tools
- OpenSwathAnalyzer
- topp - library for LC/MS data management and analysis - tools
- OpenSwathAssayGenerator
- topp - library for LC/MS data management and analysis - tools
- OpenSwathChromatogramExtractor
- topp - library for LC/MS data management and analysis - tools
- OpenSwathConfidenceScoring
- topp - library for LC/MS data management and analysis - tools
- OpenSwathDIAPreScoring
- topp - library for LC/MS data management and analysis - tools
- OpenSwathDecoyGenerator
- topp - library for LC/MS data management and analysis - tools
- OpenSwathFeatureXMLToTSV
- topp - library for LC/MS data management and analysis - tools
- OpenSwathFileSplitter
- topp - library for LC/MS data management and analysis - tools
- OpenSwathMzMLFileCacher
- topp - library for LC/MS data management and analysis - tools
- OpenSwathRTNormalizer
- topp - library for LC/MS data management and analysis - tools
- OpenSwathRewriteToFeatureXML
- topp - library for LC/MS data management and analysis - tools
- OpenSwathWorkflow
- topp - library for LC/MS data management and analysis - tools
- OrthancWSIDicomToTiff
- Whole-slide imaging support for Orthanc
- OrthancWSIDicomizer
- Whole-slide imaging support for Orthanc
- PCPCompat
- PCPCompat , pcp-collectl , pmmgr , pmwebd - backward-compatibility in the Performance Co-Pilot (PCP)
- PCPIntro
- introduction to the Performance Co-Pilot (PCP)
- PCP_KUBE_PODS
- pcp-kube-pods - list Kubernetes pods to scan for running PCP services
- PCx
- primal-dual interior-point code for linear programming
- PDFToDicomImage
- Read PDF file, and create a single or multi frame DICOM Secondary Capture image with one frame per page
- PDL::API
- making ndarrays from Perl and C/XS code
- PDL::BadValues
- Discussion of bad value support in PDL
- PDL::Broadcasting
- Tutorial for PDL's Broadcasting feature
- PDL::Course
- A journey through PDL's documentation, from beginner to advanced
- PDL::Dataflow
- - description of the dataflow implementation and philosophy
- PDL::FAQ
- Frequently asked questions about PDL
- PDL::Graphics
- Introduction to the PDL::Graphics modules
- PDL::Indexing
- Introduction to indexing and slicing ndarrays
- PDL::Internals
- description of some aspects of the current internals
- PDL::MATLAB
- A guide for MATLAB users
- PDL::Modules
- A guide to PDL's module reference
- PDL::Objects
- - Object-Orientation, what is it and how to exploit it
- PDL::PP-Inline
- Inline::Pdlpp - Write PDL Subroutines inline with PDL::PP
- PDL::PP
- Generate PDL routines from concise descriptions
- PDL::ParallelCPU
- Parallel processor multi-threading support in PDL
- PDL::Philosophy
- - Why did we write PDL?
- PDL::QuickStart
- Quick introduction to PDL features
- PDL::Scilab
- A guide for Scilab users
- PDL::Tips
- Small tidbits of useful arcana. Programming tidbits and such
- PDL::Tutorials
- A guide to PDL's tutorial documentation
- PDRFoam
- part of OpenFOAM (The Open Source CFD Toolbox)
- PDRMesh
- part of OpenFOAM (The Open Source CFD Toolbox)
- PDRblockMesh
- part of OpenFOAM (The Open Source CFD Toolbox)
- PDRsetFields
- part of OpenFOAM (The Open Source CFD Toolbox)
- PGPOOL_RESET
- restore the value of a configuration parameter to the default value
- PGPOOL_SET
- change a configuration parameter
- PGPOOL_SHOW
- show the value of a configuration parameter
- POST
- lwp-request - Simple command line user agent
- POWplot
- vizualize FITS data
- PParse
- xerces-c - xerces-c sample program
- PRICE
- image filtering and manipulation
- PSMFeatureExtractor
- topp - library for LC/MS data management and analysis - tools
- PSVIWriter
- xerces-c - xerces-c sample program
- PTAInterpolate
- Interpolate intermediate images between stereo photos
- PTBatcherGUI
- Hugin batch processor
- PTModel
- topp - library for LC/MS data management and analysis - tools
- PTPredict
- topp - library for LC/MS data management and analysis - tools
- PTblender
- Colour and brightness correction of panoramas
- PTcrop
- Crop TIFF images
- PTinfo
- Display information about a panotools-generated image
- PTmasker
- Compute stitching masks
- PTmender
- Replacement for PTStitcher