{"id":43,"date":"2013-09-26T14:58:20","date_gmt":"2013-09-26T14:58:20","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/icsf\/?page_id=43"},"modified":"2023-10-25T13:42:27","modified_gmt":"2023-10-25T13:42:27","slug":"applications","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/software\/applications\/","title":{"rendered":"Applications"},"content":{"rendered":"

Software that can be categorized as \u2018Applications\u2019, i.e., not compilers, tools etc. For a full list see the A-Z list.<\/p>\n

Bioinformatics<\/h2>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
BCFtools<\/a><\/td>\nVariant call manipulation in BCF (and VCF) files.<\/td>\n<\/tr>\n
Bedops<\/a><\/td>\nA fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n
Bedtools<\/a><\/td>\nA fast, flexible toolset for genome arithmetic.<\/td>\n<\/tr>\n
Bioconductor (in R)<\/a> <\/td>\n Tools for analysis and comprehension of high-throughput genomic data<\/td>\n<\/tr>\n
Bowtie<\/a><\/td>\nSequence alignment<\/td>\n<\/tr>\n
Bowtie2<\/a><\/td>\nSequence alignment<\/td>\n<\/tr>\n
bwa<\/a><\/td>\nBurrows-Wheeler Aligner, genome sequence mapper<\/td>\n<\/tr>\n
Cufflinks<\/a><\/td>\nSequence assembly<\/td>\n<\/tr>\n
Ensembl Tools<\/a><\/td>\nVarient Effect Predictor script in perl<\/td>\n<\/tr>\n
fgwas<\/a><\/td>\nTool for integrating functional genomic information into a GWAS<\/td>\n<\/tr>\n
Gold Suite<\/a><\/td>\nProtein Docking<\/td>\n<\/tr>\n
HiCUP<\/a><\/td>\nGenome mapping<\/td>\n<\/tr>\n
MEGAN6<\/a><\/td>\nTool for studying the taxonomic content of a set of DNA reads<\/td>\n<\/tr>\n
SAMtools<\/a><\/td>\nSequence alignment and mapping tools<\/td>\n<\/tr>\n
TADtool<\/a><\/td>\nHi-C data topological domain analysis<\/td>\n<\/tr>\n
tabix<\/a><\/td>\nGeneric indexer for TAB-delimited genome position files<\/td>\n<\/tr>\n
tophat<\/a><\/td>\nSplice junction mapper<\/td>\n<\/tr>\n
vcftools<\/a><\/td>\nPackage for working with VCFfiles<\/td>\n<\/tr>\n
jellyfish<\/a><\/td>\nA tool for fast, memory-efficient counting of k-mers in DNA.<\/td>\n<\/tr>\n<\/table>\n

Computational Chemistry, Molecular Dynamics<\/h2>\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
Gold Suite<\/a><\/td>\nProtein Docking<\/td>\n<\/tr>\n
MOE<\/a> <\/td>\n Molecular Operating Environment <\/td>\n<\/tr>\n
VMD<\/a> <\/td>\nGraphical Molecular Visualisation Tool <\/td>\n<\/tr>\n<\/table>\n

Mathematics \/ Data Analytics<\/h2>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
Anaconda Scientific Python<\/a><\/td>\nA scientific python distribution<\/td>\n<\/tr>\n
gauss<\/a><\/td>\nNumerical and statistical computation, visualization and programming<\/td>\n<\/tr>\n
IPython Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook)<\/td>\n<\/tr>\n
Julia<\/a><\/td>\nInteractive scientific programming language<\/td>\n<\/tr>\n
Jupyter Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop)<\/td>\n<\/tr>\n
MATLAB<\/a><\/td>\nNumerical computation, visualization and programming<\/td>\n<\/tr>\n
R<\/a><\/td>\nStatistical computing and graphics<\/td>\n<\/tr>\n
RStudio<\/a><\/td>\nGUI-based development environment for R<\/td>\n<\/tr>\n
SAS<\/a><\/td>\nData analysis and statistical software<\/td>\n<\/tr>\n
Stata<\/a><\/td>\nData analysis and statistical software<\/td>\n<\/tr>\n
Mplus<\/a><\/td>\nData analysis and statistical software<\/td>\n<\/tr>\n
MAUD<\/a> <\/td>\nGeneral diffraction\/reflectivity analysis primarily based on the Rietveld method<\/td>\n<\/tr>\n<\/table>\n

Programming and Development<\/h2>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
Anaconda Scientific Python<\/a><\/td>\nA scientific python distribution<\/td>\n<\/tr>\n
Clojure<\/a><\/td>\nJava-based dynamic programming language<\/td>\n<\/tr>\n
Compilers – GNU<\/a><\/td>\ngcc, g++ and gfortran<\/td>\n<\/tr>\n
gauss<\/a><\/td>\nNumerical and statistical computation, visualization and programming<\/td>\n<\/tr>\n
IPython Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook)<\/td>\n<\/tr>\n
Jupyter Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop)<\/td>\n<\/tr>\n
MATLAB<\/a><\/td>\nNumerical computation, visualization and programming<\/td>\n<\/tr>\n
NetBeans<\/a><\/td>\nJava-based IDE<\/td>\n<\/tr>\n
NetLogo<\/a><\/td>\nMulti-agent modelling environment<\/td>\n<\/tr>\n
R<\/a><\/td>\nStatistical computing and graphics<\/td>\n<\/tr>\n
RStudio<\/a><\/td>\n GUI-based development environment for R<\/td>\n<\/tr>\n
Singularity<\/a><\/td>\nContainers<\/td>\n<\/tr>\n
tensorflow<\/a><\/td>\nData flow graph processing<\/td>\n<\/tr>\n<\/table>\n

Visualization \/ Image Processing<\/h2>\n
\nSome of the application pages below include instructions on how to run the application on the iCSF GPU node (jabberwock<\/em>). Doing so will often give much better graphics performance, making the application feel more responsive and easier to use when viewing large models (e.g., finite element meshes, chemical models, X-Ray tomography 3D datasets etc.) For screenshots of some of these applications please see the iCSF GPU node page<\/a>.\n<\/div>\n\n\n\n\n\n\n\n\n\n\n\n\n
PACKAGE<\/th>\nNOTES<\/th>\n<\/tr>\n
EEGLab<\/a><\/td>\nMATLAB toolbox for EEG\/MEG data processing and viz<\/td>\n<\/tr>\n
gauss<\/a><\/td>\nNumerical and statistical computation, visualization and programming<\/td>\n<\/tr>\n
ImageJ and Fiji<\/a><\/td>\nImage processing (Java) applications.<\/td>\n<\/tr>\n
IPython Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (no longer supported, use jupyter notebook)<\/td>\n<\/tr>\n
Jupyter Notebook<\/a><\/td>\nInteractive remote execution with web-based viewing of Python (access from the nyx5,6,7 linux virtual dedktop)<\/td>\n<\/tr>\n
MATLAB<\/a><\/td>\nNumerical computation, visualization and programming<\/td>\n<\/tr>\n
MRIcroGL<\/a><\/td>\n3D GPU Medical Imaging<\/td>\n<\/tr>\n
MRIcron<\/a><\/td>\nMedical Imaging<\/td>\n<\/tr>\n
NetLogo<\/a><\/td>\nMulti-agent modelling environment<\/td>\n<\/tr>\n
VMD<\/a> <\/td>\nGraphical Molecular Visualisation Tool <\/td>\n<\/tr>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

Software that can be categorized as \u2018Applications\u2019, i.e., not compilers, tools etc. For a full list see the A-Z list. Bioinformatics PACKAGE NOTES BCFtools Variant call manipulation in BCF (and VCF) files. Bedops A fast, flexible toolset for genome arithmetic. Bedtools A fast, flexible toolset for genome arithmetic. Bioconductor (in R) Tools for analysis and comprehension of high-throughput genomic data Bowtie Sequence alignment Bowtie2 Sequence alignment bwa Burrows-Wheeler Aligner, genome sequence mapper Cufflinks Sequence assembly.. Read more »<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":13,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-43","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/comments?post=43"}],"version-history":[{"count":21,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43\/revisions"}],"predecessor-version":[{"id":1256,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/43\/revisions\/1256"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/pages\/13"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/icsf\/wp-json\/wp\/v2\/media?parent=43"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}