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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- DicomSRValidator
- Read the DICOM file specified on the command line and validate it against the standard IOD for the appropriate storage SOP Class
- DictionaryReader
- Dict client for GNUstep
- DifOdometry-Camera
- DIFODO (visual odometry method) live application
- DifOdometry-Datasets
- DIFODO (visual odometry method) from datasets
- Digestor
- topp - library for LC/MS data management and analysis - tools
- DigestorMotif
- topp - library for LC/MS data management and analysis - tools
- DiscreteHedging
- Example of using QuantLib
- DistanceEst
- Estimate distances between contigs using paired-end alignments
- Drop-seq_alignment.sh
- perform Drop-seq tagging, trimming and alignment
- DtdToHaskell
- a XML DTD to Haskell translator
- EDTSurf
- quick and accurate construction of macromolecular surfaces
- EICExtractor
- topp - library for LC/MS data management and analysis - tools
- ERPairFinder
- topp - library for LC/MS data management and analysis - tools
- ESingular
- Computer Algebra System for Polynomial Computations -- command-line interface within emacs
- ETL-config
- ETL - Get information about an ETL installation
- EdenMath
- scientific calculator for GNUstep
- Eliza
- jabber-querybot - eliza module
- EnumVal
- xerces-c - xerces-c sample program
- Epifany
- topp - library for LC/MS data management and analysis - tools
- EquityOption
- Example of using QuantLib to value equity options
- Esetroot
- eterm-utils - Eterm accessory programs
- EstimateError.py
- Calculates annotation set error rates
- Etbg
- eterm-utils - Eterm accessory programs
- Etbg_update_list
- eterm-utils - Eterm accessory programs
- Etcolors
- eterm-utils - Eterm accessory programs
- Eterm
- the Enlightened terminal emulator for the X Window System
- Etsearch
- eterm-utils - Eterm accessory programs
- Ettable
- eterm-utils - Eterm accessory programs
- EukHighConfidenceFilter
- detection of transfer RNA genes in genomic sequence
- ExecutePipeline
- topp - library for LC/MS data management and analysis - tools
- ExplicateUTF8
- Explain the status of a sequence of bytes as a UTF8 encoding
- ExternalCalibration
- topp - library for LC/MS data management and analysis - tools
- FBReader
- e-book reader
- FCluster
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- FFEval
- topp - library for LC/MS data management and analysis - tools
- FRA
- Example of using QuantLib
- FTP
- File transfer protocol application
- FalseDiscoveryRate
- topp - library for LC/MS data management and analysis - tools
- Fast5_to_seq_summary
- generate a sequencing summary like file from a directory containing Fast5 files
- FastTree
- fasttree - create phylogenetic trees from alignments of nucleotide or protein sequences
- FastaUnique
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- FeatureFinderCentroided
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderIdentification
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderIsotopeWavelet
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderMRM
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderMetabo
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderMetaboIdent
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderMultiplex
- topp - library for LC/MS data management and analysis - tools
- FeatureFinderSuperHirn
- topp - library for LC/MS data management and analysis - tools
- FeatureLinkerLabeled
- topp - library for LC/MS data management and analysis - tools
- FeatureLinkerUnlabeled
- topp - library for LC/MS data management and analysis - tools
- FeatureLinkerUnlabeledKD
- topp - library for LC/MS data management and analysis - tools
- FeatureLinkerUnlabeledQT
- topp - library for LC/MS data management and analysis - tools
- Feel
- Feel - AfterStep feel configuration
- FeelWindowBox
- FeelWindowBox - defines placement policy for certain type of windows, based on desk, window attributes, window size, etc. Useful for xinerama configurations, where windows should not be placed in between screens.
- FidoAdapter
- topp - library for LC/MS data management and analysis - tools
- FileCheck-13
- FileCheck - Flexible pattern matching file verifier
- FileCheck-14
- FileCheck - Flexible pattern matching file verifier
- FileCheck-15
- FileCheck - Flexible pattern matching file verifier
- FileCheck-16
- FileCheck - Flexible pattern matching file verifier
- FileConverter
- topp - library for LC/MS data management and analysis - tools
- FileFilter
- topp - library for LC/MS data management and analysis - tools
- FileInfo
- topp - library for LC/MS data management and analysis - tools
- FileMerger
- topp - library for LC/MS data management and analysis - tools
- FilterSeq.py
- Filters sequences in FASTA/FASTQ files
- FittedBondCurve
- Example of using QuantLib to fit discount curves
- FontManager
- manage your fonts in GNUstep
- FreeFem++-mpi
- executes FreeFem++ scripts
- FreeFem++-nw
- executes FreeFem++ scripts
- FreeFem++
- executes FreeFem++ scripts
- FreeFileSync
- a folder comparison and synchronization tool (GUI)
- Fritzing
- fritzing - from prototype to product
- Functions
- Functions - built in AfterStep functions
- FuzzyDiff
- topp - library for LC/MS data management and analysis - tools
- Fvwm2Animate
- FvwmAnimate - the fvwm animate module
- Fvwm2Auto
- FvwmAuto - the fvwm auto-raise module
- Fvwm2Backer
- FvwmBacker - the fvwm background changer module
- Fvwm2Banner
- FvwmBanner - the Fvwm Banner module
- Fvwm2Buttons
- FvwmButtons - the fvwm buttonbox module
- Fvwm2Command
- FvwmCommand - fvwm command external interface
- Fvwm2Console
- FvwmConsole - an fvwm command input interface
- Fvwm2ConsoleC.pl
- FvwmConsoleC.pl - Command editor for fvwm command input interface
- Fvwm2Cpp
- FvwmCpp - the Fvwm Cpp pre-processor
- Fvwm2Event
- FvwmEvent - the fvwm event module
- Fvwm2Form
- FvwmForm - input form module for Fvwm
- Fvwm2IconMan
- FvwmIconMan - an fvwm icon manager
- Fvwm2Ident
- FvwmIdent - the Fvwm identify-window module
- Fvwm2M4
- FvwmM4 - the fvwm M4 pre-processor
- Fvwm2Pager
- FvwmPager - the Fvwm Pager module
- Fvwm2Perl
- FvwmPerl - the fvwm perl manipulator and preprocessor
- Fvwm2Proxy
- FvwmProxy - the fvwm proxy module
- Fvwm2Rearrange
- FvwmRearrange - rearrange fvwm windows
- Fvwm2Script
- FvwmScript - module to build graphic user interface
- Fvwm3Animate
- FvwmAnimate - the fvwm animate module
- Fvwm3Auto
- FvwmAuto - the fvwm auto-raise module
- Fvwm3Backer
- FvwmBacker - the fvwm background changer module
- Fvwm3Buttons
- FvwmButtons - the fvwm buttonbox module
- Fvwm3Command
- FvwmCommand - send commands to fvwm3
- Fvwm3Console
- FvwmConsole - an fvwm command input interface
- Fvwm3Event
- FvwmEvent - the fvwm event module