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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- PToptimizer
- Wrapper around control point optimization routines
- PTroller
- Merge several images into a single one
- PTtiff2psd
- Convert a set of TIFF files into a Photoshop PSD file
- PTtiffdump
- Compare two TIFF images
- PTuncrop
- Uncrop TIFF images
- Pager
- Pager - AfterStep module for virtual desktop navigation
- PagerDecorations
- PagerDecorations - Visual attributes of the Pager window
- PairSeq.py
- Sorts and matches sequence records with matching coordinates across files
- Paje
- generic visualization tool (Gantt chart and more)
- ParaFly
- parallel command processing using OpenMP
- ParseDb.py
- Repertoire clonal assignment toolkit (Python 3)
- ParseHeaders.py
- Parses pRESTO annotations in FASTA/FASTQ sequence headers
- ParseLog.py
- Parses records in the console log of pRESTO modules
- PeakPickerHiRes
- topp - library for LC/MS data management and analysis - tools
- PeakPickerIterative
- topp - library for LC/MS data management and analysis - tools
- PeakPickerWavelet
- topp - library for LC/MS data management and analysis - tools
- PepNovoAdapter
- topp - library for LC/MS data management and analysis - tools
- PeptideIndexer
- topp - library for LC/MS data management and analysis - tools
- PerM
- perm - Efficient mapping of short reads with periodic spaced seeds If you have any usage questions, please email "yanghoch at usc dot edu"
- PercolatorAdapter
- topp - library for LC/MS data management and analysis - tools
- Perseus
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- PerseusD
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- PhosphoScoring
- topp - library for LC/MS data management and analysis - tools
- PicardCommandLine
- manipulate SAM and BAM files
- PikoPixel
- draw and edit pixel art images
- Placement
- Placement - AfterStep supports several different window placement policies. Some of them designed to fill free space, and some allowing for windows to be placed on top of others.
- Planimeter
- - compute the area of geodesic polygons
- PlopFolio
- Personal dashboard for GNUstep
- Poe
- a vorbis comment editor
- PosteRazor
- posterazor - splits an image across multiple pages for assembly into a poster
- PrecursorIonSelector
- topp - library for LC/MS data management and analysis - tools
- PrecursorMassCorrector
- topp - library for LC/MS data management and analysis - tools
- PreviSat
- previsat - satellite tracking software for observing purposes
- Preview
- General purpose image viewer for GNUstep
- ProjectCenter
- The Official GNUstep IDE
- Projucer
- the JUCE project-management tool
- ProteinInference
- topp - library for LC/MS data management and analysis - tools
- ProteinQuantifier
- topp - library for LC/MS data management and analysis - tools
- ProteinResolver
- topp - library for LC/MS data management and analysis - tools
- ProteomicsLFQ
- topp - library for LC/MS data management and analysis - tools
- Psequin
- submit sequences to Genbank, EMBL, and DDBJ
- PyroDist
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- PyroNoise
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- PyroNoiseA
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- PyroNoiseM
- AmpliconNoise - remove noise from high throughput nucleotide sequence data
- Q80_model_4_0_commandLine
- female version of 2015 risk analysis Q80_model_4_1_commandLine - male version of 2015 risk analysis
- Q80_model_4_1_commandLine
- Q80_model_4_0_commandLine - female version of 2015 risk analysis Q80_model_4_1_commandLine - male version of 2015 risk analysis
- QCCalculator
- topp - library for LC/MS data management and analysis - tools
- QCEmbedder
- topp - library for LC/MS data management and analysis - tools
- QCExporter
- topp - library for LC/MS data management and analysis - tools
- QCExtractor
- topp - library for LC/MS data management and analysis - tools
- QCImporter
- topp - library for LC/MS data management and analysis - tools
- QCMerger
- topp - library for LC/MS data management and analysis - tools
- QCShrinker
- topp - library for LC/MS data management and analysis - tools
- QFitsView
- FITS file viewer based on DPUSER
- QSO
- morse - A robotics simulator based upon the Blender Game Engine
- QTLtools-ase
- QTLtools ase - Measure ASE from RNA-seq
- QTLtools-bamstat
- QTLtools bamstat - Calculate stats of overlap between an RNAseq BAM file and an annotation
- QTLtools-cis
- QTLtools cis - cis QTL analysis
- QTLtools-correct
- QTLtools correct - Corrects genotypes or phenotypes with the provided covariates
- QTLtools-extract
- QTLtools extract - Data extraction mode
- QTLtools-fdensity
- QTLtools fdensity - Functional density around molecular QTLs
- QTLtools-fenrich
- QTLtools fenrich - Functional enrichment of molecular QTLs
- QTLtools-gwas
- QTLtools gwas - Genome-wide association tests
- QTLtools-mbv
- QTLtools mbv - Match genotypes in a VCF to a BAM file
- QTLtools-pca
- QTLtools pca - Conducts PCA
- QTLtools-quan
- QTLtools quan - Quantify gene and exon expression from RNA-seq
- QTLtools-rep
- QTLtools rep - Replicate QTL associations in an independent dataset
- QTLtools-rtc-union
- QTLtools rtc-union - Find the union of QTLs from independent datasets
- QTLtools-rtc
- QTLtools rtc - Regulatory Trait Concordance score analysis
- QTLtools-trans
- QTLtools trans - trans QTL analysis
- QTLtools
- A complete tool set for molecular QTL discovery and analysis
- QuadraticSieve
- Attempts to find a prime factor of the typed-in integer
- QualityControl
- topp - library for LC/MS data management and analysis - tools
- Querytest
- querytest.pl - Test framework without jabber connection
- R
- a language for data analysis and graphics
- REPcover
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- REPqv
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- REPtrim
- dascrubber - alignment-based scrubbing pipeline for DNA sequencing reads
- RNA2Dfold
- manual page for RNA2Dfold 2.5.1
- RNADigestor
- topp - library for LC/MS data management and analysis - tools
- RNALalifold
- manual page for RNALalifold 2.5.1
- RNALfold
- manual page for RNALfold 2.5.1
- RNAMassCalculator
- topp - library for LC/MS data management and analysis - tools
- RNAPKplex
- manual page for RNAPKplex 2.5.1
- RNAaliduplex
- manual page for RNAaliduplex 2.5.1
- RNAalifold
- manual page for RNAalifold 2.5.1
- RNAcalibrate
- calibrate statistics of secondary structure hybridisations of RNAs
- RNAcofold
- manual page for RNAcofold 2.5.1
- RNAdistance
- manual page for RNAdistance 2.5.1
- RNAdos
- manual page for RNAdos 2.5.1
- RNAduplex
- manual page for RNAduplex 2.5.1
- RNAeffective
- calculation of effective numbers of orthologous miRNA targets
- RNAeval
- manual page for RNAeval 2.5.1
- RNAfold
- manual page for RNAfold 2.5.1
- RNAheat
- manual page for RNAheat 2.5.1
- RNAhybrid
- calculate secondary structure hybridisations of RNAs
- RNAinverse
- manual page for RNAinverse 2.5.1
- RNAlocmin
- manual page for RNAlocmin 2.1.0
- RNAmultifold
- manual page for RNAmultifold 2.5.1