section 1 · User commands 💻

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C (continued)

cmtk-dof2mat(1)Degrees of freedom to matrix✨
cmtk-dwi_mask_bad_slices(1)Find bad slices in set of diffusion-weighted images.✨
cmtk-epiunwarp(1)Unwarp Echo Planar Images✨
cmtk-fib2image(1)Draw image from point coordinates of fiber tracks from .fib file.✨
cmtk-fibxform(1)Apply coordinate transformations to point coordinates in .fib file.✨
cmtk-film(1)Fix interleaved motion using inverse interpolation✨
cmtk-filter(1)Filter a volume image✨
cmtk-fit_affine_dfield(1)Fit Affine Transformation to Nonrigid Transformation✨
cmtk-fit_affine_xform(1)Fit Single Affine Transformation to Concatenated List✨
cmtk-fit_affine_xform_landmarks(1)Fit Affine Transformation to Landmarks✨
cmtk-fit_spline_dfield(1)Deformation Field to Transformation✨
cmtk-fit_spline_xform(1)Fit Single B-Spline Transformation to Concatenated Transformation List✨
cmtk-geomatch(1)Check whether the geometries (e.g., grid dimensions, pixel sizes, spatial coordinates) or two or more images match.✨
cmtk-glm(1)General Linear Model✨
cmtk-gmm(1)Gaussian mixture model segmentation✨
cmtk-gregxform(1)Apply coordinate transformations to lists of point coordinates✨
cmtk-groupwise_affine(1)Affine population registration✨
cmtk-groupwise_init(1)Affine initialization for groupwise registration✨
cmtk-groupwise_warp(1)Nonrigid population registration✨
cmtk-hausdorff(1)Hausdorff Distance.✨
cmtk-histogram(1)Image histogram✨
cmtk-imagemath(1)Image operations✨
cmtk-interleaved_bad_slices(1)Find bad slices in a time series of interleaved images (e.g., a resting-state fMRI series).✨
cmtk-iterative_shape_averaging(1)✨
cmtk-jidb(1)Fix interleaved motion using joint iterative deblurring✨
cmtk-levelset(1)Levelset segmentation✨
cmtk-lmsba(1)Local voting.✨
cmtk-lsba(1)Local voting.✨
cmtk-lvote(1)Local voting.✨
cmtk-make_initial_affine(1)Initialize affine transformation✨
cmtk-mat2dof(1)Matrix to degrees of freedom✨
cmtk-mcaffine(1)Multi-channel affine registration✨
cmtk-mcwarp(1)Multi-channel nonrigid registration✨
cmtk-mk_adni_phantom(1)Generate ADNI phantom image✨
cmtk-mk_analyze_hdr(1)Make Analyze header file✨
cmtk-mk_nifti_hdr(1)Make NIFTI header file✨
cmtk-mk_phantom_3d(1)Generate phantom image✨
cmtk-mrbias(1)MR Image Intensity Bias Field Correction✨
cmtk-overlap(1)Overlap computation✨
cmtk-probe(1)Probe image data.✨
cmtk-pxsearch(1)Search image neighborhoods for pixels.✨
cmtk-reformatx(1)Volume reformatter✨
cmtk-registration(1)Rigid and affine registration✨
cmtk-registrationx(1)Rigid and affine registration✨
cmtk-regress(1)Regression✨
cmtk-reorient(1)Reorientation✨
cmtk-sba(1)Shape-based Averaging of label images✨
cmtk-sbai(1)Shape-Based Averaging and interpolation of label images✨
cmtk-sequence(1)Value sequence✨
cmtk-similarity(1)Image similarity✨
cmtk-split(1)Split images✨
cmtk-statistics(1)Image statistics✨
cmtk-stream_pixels(1)Stream pixel data from one or more images to Standard Output.✨
cmtk-streamxform(1)Apply coordinate transformation to point coordinates from text stream.✨
cmtk-sympl(1)Symmetry plane computation✨
cmtk-symplx(1)Symmetry plane computation✨
cmtk-ttest(1)T-tests✨
cmtk-unsplit(1)Unsplit images✨
cmtk-unwarp_image_phantom(1)Create transformation to unwarp an image based on a phantom description✨
cmtk-vol2csv(1)Compute regional volumes and write to CSV file.✨
cmtk-volume_injection(1)Volume injection✨
cmtk-volume_reconstruction(1)Volume reconstruction✨
cmtk-vtkxform(1)Apply coordinate transformation to point coordinates in VTK file.✨
cmtk-warp(1)B-spline nonrigid registration✨
cmtk-warp2ps(1)Deformation to PostScript✨
cmtk-warpx(1)B-spline nonrigid registration✨
cmtk-xform2dfield(1)Transformation to Deformation Field✨
cmtk-xform2itk(1)Convert affine transformations to ITK format.✨
cmtk-xform2scalar(1)Extract scalar measures from transformations and deformation fields✨
cmucl(1)CMU Common Lisp✨
cmus(1)C* Music Player✨
cmus-remote(1)control cmus✨
cmuwmtopbm(1)convert a CMU window manager bitmap into a PBM image✨
cmx2epub(1)manual page for cmx2epub 0.9.6✨
cmx2odg(1)manual page for cmx2odg 0.9.6✨
cmx2raw(1)manual page for cmx2raw 0.1.9✨
cmx2text(1)manual page for cmx2text 0.1.9✨
cmx2xhtml(1)manual page for cmx2xhtml 0.1.9✨
Cn3D-3.0(1)a 3-dimensional viewer for biological molecules✨
cnee(1)record, replays or distributes X11 data✨
cnetz(1)http://osmocom-analog.eversberg.eu/docs/✨
cnetz_magnetic(1)http://osmocom-analog.eversberg.eu/docs/✨
cnetz_memory_card_generator(1)http://osmocom-analog.eversberg.eu/docs/✨
cnetz_sim(1)http://osmocom-analog.eversberg.eu/docs/✨
cnf(1)A command not found handler for openSUSE✨
cnn(1sr)surfraw(1) search tools✨
cnping(1)Minimal Graphical IPv4 Ping/HTTP Ping Tool✨
cnt(1)Manage systemd-nspawn containers✨
cntlm(1)authenticating HTTP(S) proxy with TCP/IP tunneling and acceleration✨
cntraining(1)character normalization training for Tesseract✨
cntsh(1)Manage systemd-nspawn containers (shell)✨
cnvgrib1to2(1)Convert a GRIB1 file to GRIB2 format✨
cnvgrib2to1(1)Convert a GRIB2 file to GRIB1 format✨
cnvkit(1)a command-line toolkit for copy number analysis.✨
cnvkit-access(1)List the locations of accessible sequence regions in a FASTA file.✨
cnvkit-antitarget(1)Derive off-target ("antitarget") bins from target regions.✨
cnvkit-autobin(1)Quickly calculate reasonable bin sizes from BAM read counts.✨
cnvkit-batch(1)Run the complete CNVkit pipeline on one or more BAM files.✨
cnvkit-bintest(1)Test for single-bin copy number alterations.✨
cnvkit-breaks(1)List the targeted genes in which a copy number breakpoint occurs.✨
cnvkit-call(1)Call copy number variants from segmented log2 ratios.✨
cnvkit-coverage(1)Calculate coverage in the given regions from BAM read depths.✨
cnvkit-diagram(1)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…✨
cnvkit-export(1)Convert CNVkit output files to another format.✨
cnvkit-fix(1)Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and re-center.✨
cnvkit-genemetrics(1)Identify targeted genes with copy number gain or loss.✨
cnvkit-heatmap(1)Plot copy number for multiple samples as a heatmap.✨
cnvkit-import-picard(1)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'…✨
cnvkit-import-rna(1)Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.✨
cnvkit-import-seg(1)Convert a SEG file to CNVkit .cns files.✨
cnvkit-import-theta(1)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.✨
cnvkit-metrics(1)Compute coverage deviations and other metrics for self- evaluation.✨
cnvkit-reference(1)Compile a coverage reference from the given files (normal samples).✨
cnvkit-reference2targets(1)Extract target and antitarget BED files from a CNVkit reference file.✨
cnvkit-scatter(1)Plot probe log2 coverages and segmentation calls together.✨
cnvkit-segment(1)Infer copy number segments from the given coverage table.✨
cnvkit-segmetrics(1)Compute segment-level metrics from bin-level log2 ratios.✨
cnvkit-sex(1)Guess samples' sex from the relative coverage of chromosomes X and Y.✨
cnvkit-target(1)Transform bait intervals into targets more suitable for CNVkit.✨
co(1)check out RCS revisions✨
co2brinepvt(1)compute and print pvt properties for co2 with brine✨
coadd(1)Co-add images for astrometry.net✨
coalChemistryFoam(1)part of OpenFOAM (The Open Source CFD Toolbox).✨
coan(1)C/C++ configuration analyser✨
coan.1(1)✨
coax(1)determine impedance of a coaxial structure, where the inner may be offset from the centre if necessary.✨
cob-config(1)manual page for cob-config 3.2.0✨
cobbler(1)Cobbler CLI Documentation✨
cobc(1)manual page for cobc 3.2.0✨
cobcrun(1)manual page for cobcrun 3.2.0✨
cobertura-check(1)show which classes do not have adequate test coverage✨
cobertura-instrument(1)add coverage instrumentation to existing classes✨
cobertura-merge(1)merge multiple data files into a single data file✨
cobertura-report(1)generate coverage reports✨
cobfusc(1)make a C source file unreadable but compilable✨
cobol_count(1)count physical lines of code, in each input file✨
cobra(1)A generator for Cobra based Applications✨
cobra-add(1)Add a command to a Cobra Application✨
cobra-cli(1)A generator for Cobra-based Go Applications✨
cobra-cli-add(1)Add a command to a Cobra Application✨
cobra-cli-init(1)Initialize a Cobra Application✨
cobra-init(1)Initialize a Cobra Application✨
coccigrep(1)semantic grep for the C programming language✨
coccinella(1)a Jabber based IM client with integrated whiteboard✨
cockpit(1)Cockpit✨
cockpit-bridge(1)Cockpit Host Bridge✨
cockpit-desktop(1)Cockpit Desktop integration✨
cococpp(1)Coco/R Compiler Generator (C++ Version)✨
cococs(1)Coco/R Compiler Generator (C-Sharp Version)✨
cocoj(1)Coco/R Compiler Generator (Java Version)✨
cocotb-config(1)Query cocotb configuration✨
cod-tools-version(1)print the version of cod-tools package.✨
cod2rdf(1)describe (in RDF format) properties of COD structures.✨
cod_fetch(1)query COD server using the Perl DBD::mysql interface.✨
cod_manage_related(1)embed provided relationships between databases into a CIF file using the COD notation described in the 'cod_cif.dic' dictionary.✨
codb2json(1)convert CANopen Profile data base (codb) files to JSON format✨
codcif2sdf(1)convert CIFs with crystal description (similar to those obtained from the COD) to an SDF file with a molecule description. Intended to be suitable for upload to PubChem.✨
codcmp(1e)Codon usage table comparison✨
codcopy(1e)Copy and reformat a codon usage table✨
code-minimap(1)Generate minimap of source code✨
code2html(1)Converts a program source code to HTML✨
code_saturne(1)Main user script of Code_Saturne.✨
codeblocks(1)The open-source, cross-platform IDE✨
codecgraph(1)hda-intel codec graph generator✨
codechanges(1)computes the amount of code changes between two code trees or single files✨
codegroup(1)encode / decode binary file as five letter codegroups✨
codelite(1)a lightweight and powerful C/C++ IDE✨
codelite-make(1)a makefile generator based on CodeLite's workspace✨
codelite_fix_files(1)convert a CodeLite project and workspace from the DOS environment to the *nix environment✨
codelite_open_helper(1)Helper script to load a file from the command line.✨
codepage(1)extract a codepage from an MSDOS codepage file✨
codequery(1)create codequery database✨
coderay(1)scans a file and generates syntax-highlighted html output✨
coderay_stylesheet(1)output the default cascading stylesheet used by CodeRay.✨
coderet(1e)Extract CDS, mRNA and translations from feature tables✨
codes_bufr_filter(1)manual page for codes_bufr_filter✨
codes_config(1)manual page for codes_config 2.50.0✨
codes_export_resource(1)manual page for Usage: redhat-linux- build/bin/codes_export_resource [-s | -d] resource_path out_file✨
codes_info(1)manual page for codes_info✨
codes_parser(1)manual page for --version ... FAILED✨
codes_split_file(1)manual page for Usage: redhat-linux-build/bin/codes_split_file [-v] nchunks infile✨
codesearch(1)Debian Codesearch CLI tool✨
codesign_allocate(1)add code signing data to a Mach-O file✨
codesnippets(1)Stand-alone app for the codesnippets Code::Blocks plugin.✨
codespell(1)detect spelling mistakes in source code✨
codfis(1)tool to generate Italian fiscal codes✨
codonw(1)Correspondence Analysis of Codon Usage✨
codonw-aau(1)calculate Amino Acid Usage (AAU)✨
codonw-base3s(1)silent base G+C+A+T calculating program✨
codonw-bases(1)detailed report of base composition✨
codonw-cai(1)calculate Codon Adaptation Index (CAI)✨
codonw-cbi(1)calculate Codon Bias Index (CBI)✨
codonw-cu(1)calculate codon usage✨
codonw-cutab(1)tabulation of codon usage✨
codonw-cutot(1)tabulation of datasets codon usage✨
codonw-dinuc(1)dinucleotide usage of the three codon positions✨
codonw-enc(1)calculate Effective Number of Codons (ENc)✨
codonw-fop(1)calculate Frequency of OPtimal codons index (FOP)✨
codonw-gc(1)G+C content of gene (all 3 codon positions)✨
codonw-gc3s(1)GC of synonymous codons 3rd positions✨