1 User commands
66,310 pages in section 1.
cm
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cmWork with configs. -
cm2hmm -
cm2hmmsearch -
cm2htmlconvert CommonMark file to HTML document -
cm2latexconvert CommonMark file to LaTeX source -
cm2manconvert CommonMark file to man page -
cm2pseudoxmlconvert CommonMark file to pseudo-XML document -
cm2remConvert Sun's "cm" input file to Remind format -
cm2rem.Convert Sun's "cm" input file to Remind formattcl -
cm2xetexconvert CommonMark file to XeTeX source -
cm2xmlconvert CommonMark file to XML document -
cm_helper for wigeon (Pintail 16S DNA anomaly detection)to_ wigeon -
cmafiheLojban word glosser -
cmakeCMake Command-Line Reference -
cmake-Parse cmake listfiles and re-emit them with semantic annotations in HTML.annotate -
cmake-Parse cmake listfiles and format them nicely.format -
cmake-Parse cmake listfiles, find function and macro declarations, and generate parsers for them.genparsers -
cmake-CMake GUI Command-Line Referencegui -
cmake-Check cmake listfile for lintlint -
cmakecommandsReference of available CMake commands. -
cmakecompatReference of CMake compatibility commands. -
cmakemodulesReference of available CMake modules. -
cmakepoliciesReference of CMake policies. -
cmakepropsReference of CMake properties. -
CMakeCross-platform MakeSetup -
cmaketestCross-platform Makefile generator. -
cmakevarsReference of CMake variables. -
cmalignalign sequences to a covariance model -
cmap2encconvert glyph indices in a TrueType-flavored OpenType font to Adobe glyph names -
cmarkconvert CommonMark formatted text to HTML -
cmark-pure Python script parser for the CommonMark Markdown specbkrs -
cmark-convert CommonMark formatted text with GitHub Flavored Markdown extensions to HTMLgfm -
cmatrix -
cmbuildconstruct covariance model(s) from structurally annotated RNA multiple sequence alignment(s) -
cmcalibratefit exponential tails for covariance model E-value determination -
CMCEnrollUsed to sign a certificate request with an agent's certificate. Note: This tool has not yet been updated to work with the latest improvement in the CA to conform to RFC 5272. Please use CMCRequest instead. -
cmconvertconvert Infernal covariance model files -
CMCRequestUsed to generate a CMC certificate issuance or revocation request. -
CMCResponseUsed to parse CMC responses returned from CMC issuance or revocation requests. -
CMCSharedUsed to process a user passphrase and create shared token to be stored by the CA to allow Shared Secret-based proof of origin in cases such as CMC certificate issuance and revocation.Token -
cmddumpsimulated TRS-80 CMD file loader -
cmdebugReports the status of a host Cache Manager -
cmdlinerHelper tool for cmdliner based tools -
cmdliner-Output generic completion scriptsgeneric- completion -
cmdliner-Install support files for cmdliner toolsinstall -
cmdliner-Install generic completion scriptsinstall- generic- completion -
cmdliner-Install tool completion scriptsinstall- tool- completion -
cmdliner-Install tool and subcommand manpagesinstall- tool- manpages -
cmdliner-Install both tool completion and manpagesinstall- tool- support -
cmdliner-Output all subcommands of a cmdliner tooltool- commands -
cmdliner-Output tool completion scriptstool- completion -
cmdtestblackbox testing of Unix command line tools -
cmdtoolrun a shell (or other program) in an OpenWindows enhanced terminal window -
cmemitsample sequences from a covariance model -
CMEncryptSend Encrypted Payload -
cmewcreate Mew's database file -
cmfetchretrieve covariance model(s) from a file -
cmgenfilament material tools -
cmigemoC/Migemo Library 1.3 Driver -
cmigrepsearch in ocaml compiled interface files -
cmis-command line CMIS client tool.client -
cmixThe C-Mix/II program specializer -
cmixshowbrowser for C-Mix/II feedback output -
cmkdircreate encrypted directory for CFS -
cmkkeycreate secondary copy of CFS directory key -
cmml-transforms a sloppily written CMML instance document into a valid one.fix -
cmml-Apply a timeshift to all the clip tags.timeshift -
cmml-validates a CMML instance document against the cmml.dtd and some further rules.validate -
cmpcompare two files byte by byte -
cmphminimum perfect hashing tool -
cmph5toolstoolkit for command-line tools associated with cmp.h5 file processing -
cmph5tools.toolkit for command-line tools associated with cmp.h5 file processingpy -
cmppCode Model PreProcessor -
cmpressprepare a covariance model database for cmscan -
cmrgNo manpage for this program, utility or function. -
cmscansearch sequence(s) against a covariance model database -
cmscore -
cmsearchsearch covariance model(s) against a sequence database -
cmstConnman System Tray -
cmstatsummary statistics for a covariance model file -
cmsutilPerforms basic cryptograpic operations, such as encryption and decryption, on Cryptographic Message Syntax (CMS) messages. -
cmtimeRDMA CM connection steps timing test. -
cmtkthe Computational Morphometry Toolkit -
cmtk-Atlas-based segmentationasegment -
cmtk-Segmentation using SRI24 atlasasegment_ sri24 -
cmtk-Average affine transformationsaverage_ affine -
cmtk-Average imagesaverage_ images -
cmtk-Label image averagingaverage_ labels -
cmtk-Average using ADMavg_ adm -
cmtk-Concatenate affine transformationsconcat_ affine -
cmtk-Convert nonrigd transformations.convert_ warp -
cmtk-Convert between image file formats and data types.convertx -
cmtk-Image/transformation database maintenance and query tooldbtool -
cmtk-DICOM to Imagedcm2image -
cmtk-Describe image and transformation file formats and parametersdescribe -
cmtk-Destripe volume image data.destripe -
cmtk-Detect ADNI phantom landmarks in phantom imagedetect_ adni_ phantom -
cmtk-Detect spheresdetect_ spheres_ matched_ filter -
cmtk-Degrees of freedom to matrixdof2mat -
cmtk-Find bad slices in set of diffusion-weighted images.dwi_ mask_ bad_ slices -
cmtk-Unwarp Echo Planar Imagesepiunwarp -
cmtk-Draw image from point coordinates of fiber tracks from .fib file.fib2image -
cmtk-Apply coordinate transformations to point coordinates in .fib file.fibxform -
cmtk-Fix interleaved motion using inverse interpolationfilm -
cmtk-Filter a volume imagefilter -
cmtk-Fit Affine Transformation to Nonrigid Transformationfit_ affine_ dfield -
cmtk-Fit Single Affine Transformation to Concatenated Listfit_ affine_ xform -
cmtk-Fit Affine Transformation to Landmarksfit_ affine_ xform_ landmarks -
cmtk-Deformation Field to Transformationfit_ spline_ dfield -
cmtk-Fit Single B-Spline Transformation to Concatenated Transformation Listfit_ spline_ xform -
cmtk-Fusion viewer.fview -
cmtk-Check whether the geometries (e.g., grid dimensions, pixel sizes, spatial coordinates) or two or more images match.geomatch -
cmtk-General Linear Modelglm -
cmtk-Gaussian mixture model segmentationgmm -
cmtk-Apply coordinate transformations to lists of point coordinatesgregxform -
cmtk-Affine population registrationgroupwise_ affine -
cmtk-Affine initialization for groupwise registrationgroupwise_ init -
cmtk-Nonrigid population registrationgroupwise_ warp -
cmtk-Hausdorff Distance.hausdorff -
cmtk-Image histogramhistogram -
cmtk-Image operationsimagemath -
cmtk-Find bad slices in a time series of interleaved images (e.g., a resting-state fMRI series).interleaved_ bad_ slices -
cmtk-iterative_ shape_ averaging -
cmtk-Fix interleaved motion using joint iterative deblurringjidb -
cmtk-Levelset segmentationlevelset -
cmtk-Local voting.lmsba -
cmtk-Local voting.lsba -
cmtk-Local voting.lvote -
cmtk-Initialize affine transformationmake_ initial_ affine -
cmtk-Matrix to degrees of freedommat2dof -
cmtk-Multi-channel affine registrationmcaffine -
cmtk-Multi-channel nonrigid registrationmcwarp -
cmtk-Generate ADNI phantom imagemk_ adni_ phantom -
cmtk-Make Analyze header filemk_ analyze_ hdr -
cmtk-Make NIFTI header filemk_ nifti_ hdr -
cmtk-Generate phantom imagemk_ phantom_ 3d -
cmtk-MR Image Intensity Bias Field Correctionmrbias -
cmtk-Overlap computationoverlap -
cmtk-Probe image data.probe -
cmtk-Search image neighborhoods for pixels.pxsearch -
cmtk-Volume reformatterreformatx -
cmtk-Rigid and affine registrationregistration -
cmtk-Rigid and affine registrationregistrationx -
cmtk-Regressionregress -
cmtk-Reorientationreorient -
cmtk-Shape-based Averaging of label imagessba -
cmtk-Shape-Based Averaging and interpolation of label imagessbai -
cmtk-Value sequencesequence -
cmtk-Image similaritysimilarity -
cmtk-Split imagessplit -
cmtk-Image statisticsstatistics -
cmtk-Stream pixel data from one or more images to Standard Output.stream_ pixels -
cmtk-Apply coordinate transformation to point coordinates from text stream.streamxform -
cmtk-Symmetry plane computationsympl -
cmtk-Symmetry plane computationsymplx -
cmtk-T-teststtest -
cmtk-Unsplit imagesunsplit -
cmtk-Create transformation to unwarp an image based on a phantom descriptionunwarp_ image_ phantom -
cmtk-Compute regional volumes and write to CSV file.vol2csv -
cmtk-Volume injectionvolume_ injection -
cmtk-Volume reconstructionvolume_ reconstruction -
cmtk-Apply coordinate transformation to point coordinates in VTK file.vtkxform -
cmtk-B-spline nonrigid registrationwarp -
cmtk-Deformation to PostScriptwarp2ps -
cmtk-B-spline nonrigid registrationwarpx -
cmtk-Transformation to Deformation Fieldxform2dfield -
cmtk-Convert affine transformations to ITK format.xform2itk -
cmtk-Extract scalar measures from transformations and deformation fieldsxform2scalar -
cmuclCMU Common Lisp programming environment -
cmucl-CMU Common Lisplisp -
cmucl-wrapper script to execute cmucl fasls nativelyrun -
cmusC* Music Player -
cmus-control cmusremote -
cmuwmtopbmconvert a CMU window manager bitmap into a PBM image
cn
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Cn3Da 3-dimensional viewer for biological molecules -
Cn3D-a 3-dimensional viewer for biological molecules3. 0 -
cneerecord, replays or distributes X11 data -
cnetworkmanagerCommand-line client for NetworkManager. -
cnetzhttp://osmocom-analog.eversberg.eu/docs/ -
cnetz_http://osmocom-analog.eversberg.eu/docs/magnetic -
cnetz_http://osmocom-analog.eversberg.eu/docs/memory_ card_ generator -
cnetz_http://osmocom-analog.eversberg.eu/docs/sim -
cnid_check and repair Netatalk CNID database indexesindex -
cnna fast unix command line interface to WWW services -
cnrun -
cntManage systemd-nspawn containers -
cntlmauthenticating HTTP(S) proxy with TCP/IP tunneling and acceleration -
cntrainingcharacter normalization training for Tesseract -
cntshManage systemd-nspawn containers (shell) -
cnvgrib1to2Convert a GRIB1 file to GRIB2 format -
cnvgrib2to1Convert a GRIB2 file to GRIB1 format -
cnvkita command-line toolkit for copy number analysis. -
cnvkit-List the locations of accessible sequence regions in a FASTA file.access -
cnvkit-Derive off-target ("antitarget") bins from target regions.antitarget -
cnvkit-Quickly calculate reasonable bin sizes from BAM read counts.autobin -
cnvkit-Run the complete CNVkit pipeline on one or more BAM files.batch -
cnvkit-Test for single-bin copy number alterations.bintest -
cnvkit-List the targeted genes in which a copy number breakpoint occurs.breaks -
cnvkit-Call copy number variants from segmented log2 ratios.call -
cnvkit-Calculate coverage in the given regions from BAM read depths.coverage -
cnvkit-Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the right side).diagram -
cnvkit-Convert CNVkit output files to another format.export -
cnvkit-Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and re-center.fix -
cnvkit-Identify targeted genes with copy number gain or loss.genemetrics -
cnvkit-Plot copy number for multiple samples as a heatmap.heatmap -
cnvkit-Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files. The input file is generated by the PER_TARGET_COVERAGE option in the CalculateHsMetrics script in Picard tools. If 'antitarget' is in the input filename, the generated output filename will have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'.import- picard -
cnvkit-Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.import- rna -
cnvkit-Convert a SEG file to CNVkit .cns files.import- seg -
cnvkit-Convert THetA output to a BED-like, CNVkit-like tabular format. Equivalently, use the THetA results file to convert CNVkit .cns segments to integer copy number calls.import- theta -
cnvkit-Compute coverage deviations and other metrics for self-evaluation.metrics -
cnvkit-Compile a coverage reference from the given files (normal samples).reference -
cnvkit-Extract target and antitarget BED files from a CNVkit reference file.reference2targets -
cnvkit-Plot probe log2 coverages and segmentation calls together.scatter -
cnvkit-Infer copy number segments from the given coverage table.segment -
cnvkit-Compute segment-level metrics from bin-level log2 ratios.segmetrics -
cnvkit-Guess samples' sex from the relative coverage of chromosomes X and Y.sex -
cnvkit-Transform bait intervals into targets more suitable for CNVkit.target