1 r our proposed method has been developed and
is freely available.
2 nally efficient implementation of our method
is freely available.
3 incorporated into a searchable database that
is freely available.
4 ftware underlying our method, Coalescenator,
is freely available.
5 The BioNetFit source code (Perl)
is freely available.
6 The Cell Component Ontology
is freely available.
7 The relevant software
is freely available.
8 integrated analysis and visualization tools
are freely available.
9 All software
are freely available.
10 ware and sample databases with documentation
are freely available.
11 All iAnn widgets
are freely available.
12 The annotations, as well as the HPO itself,
are freely available.
13 The datasets created in this paper will
be freely available after publication.
14 Annotations from GOA
are freely available and are accessible through a powerf
15 The database
is freely available and can be easily scaled and updated
16 pong
is freely available and can be installed using the Pytho
17 It
is freely available and encompasses stand-alone scripts
18 COCONUT
is freely available and provides a graphical user interf
19 CLIME
is freely available and should become increasingly power
20 nome-wide developmental enhancer predictions
are freely available as a UCSC Genome Browser track, whi
21 e algorithm and a wealth of related features
are freely available as R-package enviPat and as a user-
22 Software will
be freely available as the OriGen package in R.
23 The HaploPOP software
is freely available as a command-line software at www.ie
24 Twine
is freely available as a compiled Java .jar package or J
25 An implementation
is freely available as a Cytoscape app.
26 Our framework, named METRADE,
is freely available as a MATLAB toolbox.
27 mining K in complex biological datasets, and
is freely available as a package for R.
28 It
is freely available as a precompiled binary package for
29 3 license and
is freely available as a standalone program or as a tool
30 FTFlex
is freely available as a web-based server at http://ftfl
31 DynaMet
is freely available as an extension package for Python b
32 The tool
is freely available as an R package (CorrectOverloadedPe
33 DMRMark
is freely available as an R package at the CRAN R packag
34 FEM
is freely available as an R-package from http://sourcefo
35 phenoVein
is freely available as open-source software.
36 BEAT
is freely available as part of Bioconductor at www.bioco
37 The updated version of TurboFold II
is freely available as part of the RNAstructure software
38 The software and computed UHSs
are freely available at github.com/Shamir-Lab/DOCKS/ and
39 customProDB and related documents
are freely available at http://bioconductor.org/packages
40 documentation and installation instructions
are freely available at http://epock.bitbucket.org.
41 on and source code for the HAL API and tools
are freely available at http://github.com/glennhickey/ha
42 code, binaries, documentation and tutorials
are freely available at http://johnmay.github.com/meting
43 PFP/ESG servers
are freely available at http://kiharalab.org/web/pfp.php
44 The database and web server
are freely available at http://prodata.swmed.edu/M2S/mut
45 the models for human and many other species
are freely available at http://repeatmasker.org/garlic/.
46 of the proposed method, and its source code
are freely available at http://www.cs.columbia.edu/~pier
47 The package and additional documentation
are freely available at https://bitbucket.org/benhamlab/
48 The Java source code and the library
are freely available at https://github.com/loopasam/Brai
49 PSIKO and accompanying manual
are freely available at https://www.uea.ac.uk/computing/
50 All tools and data
are freely available at PATRIC.
51 Our Python tools
are freely available at www.cs.hmc.edu/ approximately ha
52 series and associated educational materials
are freely available at www.rcsb.org.
53 ource code and a comprehensive user's manual
are freely available at: http://crossmap.sourceforge.net
54 The algorithm and sample data described here
are freely available at: http://opencobra.sourceforge.ne
55 An R package will
be freely available at CRAN and www.stjuderesearch.org/s
56 ++ with OpenMP (optional at compilation) and
is freely available at 'www.stat.ucla.edu/ approximately
57 as a part of SPAdes genome assembler, which
is freely available at bioinf.spbau.ru/en/spades.
58 The package
is freely available at CRAN for easy installation, and a
59 The software
is freely available at github.com/BioContainers/.
60 be accessed at www.foldatlas.com Source code
is freely available at github.com/mnori/foldatlas under
61 TEMP
is freely available at github: https://github.com/JialiU
62 DeconRNASeq is written in R, and
is freely available at http://bioconductor.org/packages.
63 The program of DRAGEN
is freely available at http://bioinfo.au.tsinghua.edu.cn
64 A SPOCS web application
is freely available at http://cbb.pnnl.gov/portal/tools/
65 ChEpiMod
is freely available at http://chepimod.org.
66 Source code and documentation
is freely available at http://code.google.com/p/biopax-p
67 c software package including the source code
is freely available at http://cssb.biology.gatech.edu/AP
68 The SIOMICS software
is freely available at http://eecs.ucf.edu/ approximatel
69 lemented in PHP, Java, MySQL and Apache, and
is freely available at http://evpedia.info.
70 SAMNetWeb
is freely available at http://fraenkel.mit.edu/samnetweb
71 Our tool VGA
is freely available at http://genetics.cs.ucla.edu/vga/
72 It
is freely available at http://magi.ucsd.edu.
73 The package
is freely available at http://mnmccall.com/software and
74 d beta-barrel types of membrane proteins and
is freely available at http://opig.stats.ox.ac.uk/webapp
75 ParseCNV
is freely available at http://parsecnv.sourceforge.net.
76 NetVenn
is freely available at http://probes.pw.usda.gov/NetVenn
77 as part of UCSF Chimera release 1.10, which
is freely available at http://rbvi.ucsf.edu/chimera/down
78 The DNAshape web server
is freely available at http://rohslab.cmb.usc.edu/DNAsha
79 Arpeggio
is freely available at http://sourceforge.net/p/arpeggio
80 GRASP is implemented in GNU C++, and
is freely available at http://sourceforge.net/projects/g
81 Kinannote
is freely available at http://sourceforge.net/projects/k
82 Software was implemented in C++ and
is freely available at http://sourceforge.net/projects/l
83 The ValiDichro server
is freely available at http://valispec.cryst.bbk.ac.uk/c
84 ependent Matlab implementation of the method
is freely available at http://www.ee.kth.se/ctsoftware;
85 The code
is freely available at http://www.epcc.ed.ac.uk/software
86 The source code
is freely available at http://www.healthcare.uiowa.edu/l
87 The method is implemented in R and
is freely available at http://www.pitt.edu/~mchikina/BIR
88 The source code of the program
is freely available at http://www.stats.ox.ac.uk/researc
89 iPEAP
is freely available at http://www.tongji.edu.cn/ approxi
90 TRES
is freely available at http://www.tres.roslin.ed.ac.uk.
91 The package
is freely available at http://zhoulab.usc.edu/Hi-Correct
92 and implementation: A Python implementation
is freely available at https://bitbucket.org/wanding/dup
93 Hydra-Multi is written in C++ and
is freely available at https://github.com/arq5x/Hydra.
94 A code package implementing the strategy
is freely available at https://github.com/HongjieZhu/CIM
95 The C++ source code implementing TrioDeNovo
is freely available at https://medschool.vanderbilt.edu/
96 FineSplice
is freely available at https://sourceforge.net/p/finespl
97 Source code
is freely available at https://sourceforge.net/projects/
98 ASPeak implementation
is freely available at https://sourceforge.net/projects/
99 Literome
is freely available at literome.azurewebsites.net.
100 The rMATS source code
is freely available at rnaseq-mats.sourceforge.net/.
101 ToxDock
is freely available at rosie.rosettacommons.org/tox_dock
102 Software for calculating UPCs
is freely available at www.bioconductor.org/packages/rel
103 GeneSense
is freely available at www.biomedsense.org/genesense.php
104 e high-throughput phylogenomic analyses, and
is freely available at www.currielab.wisc.edu/downloads.
105 CLIC
is freely available at www.gene-clic.org.
106 plemented in Python, Perl and Javascript and
is freely available at www.genomegeek.com and www.sanger
107 Clonify
is freely available at www.github.com/briney/clonify-pyt
108 DeepSite
is freely available at www.playmolecule.org.
109 PLUMED-ISDB
is freely available at www.plumed.org.
110 The WGE database
is freely available at www.sanger.ac.uk/htgt/wge
111 CPAG
is freely available at www.sourceforge.net/projects/CPAG
112 BSeQC
is freely available at: http://code.google.com/p/bseqc/.
113 Our tool KmerGenie
is freely available at: http://kmergenie.bx.psu.edu/.
114 The package
is freely available at: http://lin.uestc.edu.cn/server/p
115 VisANT
is freely available at: http://visant.bu.edu.
116 DCB is an open source Web-based tool that
is freely available at: http://www.maayanlab.net/LINCS/D
117 The Ragout software
is freely available at: https://github.com/fenderglass/R
118 Our source code
is freely available at: https://github.com/kuleshov/Prob
119 The software
is freely available at: tanto.bioe.uic.edu/m-DiSGro.
120 All HPC-7 data sets
are freely available both through standard repositories
121 QwikMD
is freely available by download on group and personal co
122 nments like MATLAB, and all its dependencies
are freely available for academic users.
123 GPMDB data and database tables
are freely available for commercial and non-commercial u
124 These data
are freely available for download and visualization onli
125 The DECIPHER R package and source code
are freely available for download at DECIPHER.cee.wisc.e
126 The source code and binary files
are freely available for download at http://a-kramer.git
127 Source code and compiled package
are freely available for download at http://apps.cytosca
128 Source code and binaries
are freely available for download at http://apps.cytosca
129 The tools
are freely available for download at http://bioinformati
130 code and binaries of the R package RVsharing
are freely available for download at http://cran.r-proje
131 Source code and documentation
are freely available for download at https://github.com/
132 ode and the datasets used in our experiments
are freely available for future comparison at http://www
133 AB code and datasets used in our experiments
are freely available for future comparison at http://www
134 nsive additional documentation and tutorials
are freely available for Linux, Mac and Windows: http://
135 Executable versions of the program
are freely available for Mac OSX and Windows operating s
136 The implementations
are freely available for non-commercial purposes.
137 lity and implementation: The implementations
are freely available for non-commercial purposes.
138 The implementations
are freely available for non-commercial purposes.
139 ware downloads and installation instructions
are freely available for non-commercial use at https://g
140 ded in ngsTools are implemented in C/C++ and
are freely available for noncommercial use at https://gi
141 The gCMAP and gCMAPWeb R packages
are freely available for UNIX, Windows and Mac OS X oper
142 The software
is freely available for academic laboratories.
143 The Pathway Tools software
is freely available for academic research and is availab
144 he implemented multi-threading software FISH
is freely available for academic use at https://sites.go
145 sgnesR
is freely available for academic use.
146 1000 Genomes Project and other projects and
is freely available for academic use.
147 pRESTO
is freely available for academic use.
148 NetBioV
is freely available for academic use.
149 s with the 64 bit Linux operating system and
is freely available for academic use.
150 is a highly sensitive and accurate tool that
is freely available for academic use.
151 TCGA SpliceSeq
is freely available for academic, government or commerci
152 fmcsR
is freely available for all common operating systems fro
153 systemPipeR
is freely available for all common operating systems fro
154 available web services, the code for ePlant
is freely available for any other biological species res
155 Software
is freely available for download at genetics.cs.ucla.edu
156 The software
is freely available for download at github.com/sanger-pa
157 lign source code (implemented mainly in C++)
is freely available for download at http://bioen-compbio
158 The software
is freely available for download at http://genetics.cs.u
159 PhyloSNP
is freely available for download at http://hive.biochemi
160 Source code
is freely available for download at http://indra.mullins
161 Source code
is freely available for download at http://lobstah.bu.ed
162 The package TREAT
is freely available for download at http://www.hanzhang.
163 HApredictor
is freely available for download at http://www.ncbi.nlm.
164 ova is open source under the MIT license and
is freely available for download at https://github.com/c
165 ented in a combination of Java and C/C++ and
is freely available for download at https://github.com/m
166 ted in Perl, C/C++ and Java, the source code
is freely available for download at the VISTA Web site:
167 r the GNU general public license (version 3)
is freely available for download from http://smithlabres
168 SNPlice
is freely available for download from https://code.googl
169 InterProScan
is freely available for download from the EMBl-EBI FTP s
170 The software
is freely available for download.
171 ATHENA
is freely available for download.
172 Our software
is freely available for non-commercial purposes from our
173 The SinCHet software
is freely available for non-profit academic use.
174 Our tool
is freely available for noncommercial use at http://www.
175 IsoMS for Windows running R
is freely available for noncommercial use from www.mycom
176 The web server
is freely available for public use at: http://rna.urmc.r
177 While XCMS-based software
is freely available for untargeted analysis of mass spec
178 The TargetRNA2 web server
is freely available for use at http://cs.wellesley.edu/
179 WebProtege
is freely available for use on the Web at http://webprot
180 thousand different tools and resources that
are freely available from a large range of life science
181 e software, documentation and demonstrations
are freely available from http://trinityrnaseq.sourcefor
182 All information and data
are freely available from our website at https://www.vec
183 urce code and documentation of the framework
are freely available from the project web site.
184 rated the method into R package ENmix, which
is freely available from Bioconductor website.
185 The 'switchBox' package
is freely available from Bioconductor: http://www.biocon
186 is part of R package InfiniumPurify , which
is freely available from CRAN.
187 bly into existing metabolomics pipelines and
is freely available from CRAN.
188 ed under the Lesser GPL, and the source code
is freely available from GitHub.
189 GeneFriends
is freely available from http://www.GeneFriends.org and
190 R code to compute the GRV test
is freely available from http://www2.imperial.ac.uk/ app
191 Source code
is freely available from https://bitbucket.org/andreyto/
192 ped with a graphical user interface, GENFIRE
is freely available from our website and is expected to
193 RCSB PDB Mobile
is freely available from the Apple App Store and Google
194 d the method into the R package ENmix, which
is freely available from the Bioconductor website.
195 EILA is implemented as an R package, which
is freely available from the Comprehensive R Archive Net
196 proach is implemented in an R package, which
is freely available from the corresponding author.
197 The cit open-source R package
is freely available from the CRAN website with embedded
198 KODAMA
is freely available from the R archive CRAN.
199 EBglmnet package
is freely available from the R archive CRAN.
200 mplemented using a combination of Java and R
is freely available from the website at http://humangeno
201 TCW
is freely available from www.agcol.arizona.edu/software/
202 The software tool, implemented in C and R,
is freely available from www.popgen.dk/software.
203 om general English and biomedical literature
are freely available;
however, their validity as a subst
204 The data
are freely available in a public resource to foster diag
205 -to-date collection of trait-associated SNPs
are freely available in Bioconductor
206 ter research community, the genomic variants
are freely available in different formats and from multi
207 Tools to perform MultiBLUP
are freely available in our software LDAK.
208 Currently >2500 foods in 22 food groups
are freely available in various NZFCDB output products o
209 MIST will
be freely available in the OASIS R package at http://www
210 It
is freely available in 20 countries (iOS and Android pla
211 PINBPA app
is freely available in Cytoscape app store.
212 Source code
is freely available in Github at https://www.github.com/
213 Modified Bin Aggolmeration
is freely available in MSpire, an open source mass spect
214 ode for implementing lossless data reduction
is freely available in the Appendix.
215 All programs
are freely available on SourceForge.
216 h all source code and a detailed usage guide
are freely available on Sourceforge.
217 package is written in R, is open source and
is freely available on CRAN and from netweavers.erasmusm
218 FlowClus
is freely available on GitHub (jsh58/FlowClus); it is wr
219 Source code
is freely available on GitHub under a GNU General Public
220 KCMBT
is freely available on GitHub:.
221 gKaKs is implemented in Perl and
is freely available on http://longlab.uchicago.edu/?q=gK
222 samples and a simple software algorithm that
is freely available on our laboratory Web site.
223 Software
is freely available on request.
224 tcpl
is freely available on the Comprehensive R Archive Netwo
225 It
is freely available on the Ensembl browser, from the Ens
226 The software
is freely available on the SourceForge website http://lu
227 GlycoPattern
is freely available on the Web at http://glycopattern.em
228 INstruct
is freely available on the web at http://instruct.yulab.
229 miRCancer
is freely available on the web at http://mircancer.ecu.e
230 STAR browser system
is freely available on the web at http://wanglab.ucsd.ed
231 HippDB
is freely available on the web at http://www.nyu.edu/pro
232 PEASE
is freely available on the web at www.ofranlab.org/PEASE
233 R code to perform the RASTA procedures
is freely available on the web at www.stat.purdue.edu/ a
234 arized factor graph for parameter estimation
are freely available online at http://ctsb.is.wfubmc.edu
235 The Mobyle SNAP Workbench portal
is freely available online at http://snap.hpc.ncsu.edu/.
236 T-lex2
is freely available online at http://sourceforge.net/pro
237 The entire Database Issue
is freely available online on the Nucleic Acids Research
238 The entire Database Issue
is freely available online on the Nucleic Acids Research
239 ogical, psychological and pathological) that
is freely available online.
240 CRISPulator
is freely available online.
241 This software
is freely available only for noncommercial users.
242 Goldilocks
is freely available open-source software distributed und
243 lable to generate linkage map graphics, none
are freely available,
produce publication quality figure
244 we have collected and the phenotypes scored
are freely available through the project website.
245 Census
is freely available through our updated single-cell anal
246 Our algorithm
is freely available through our web server and solves mo
247 gkmSVM package
is freely available through the Comprehensive R Archive
248 Software
is freely available through the Evol component of ProDy
249 The data
are freely available to accessors either as single files
250 Java source and executable code
are freely available to non-commercial users at http://p
251 genomic alignment data and computer programs
are freely available to noncommercial users from http://
252 The GDI server, data, and software
are freely available to noncommercial users from lab.roc
253 the biology of HGSC, and the ID8 cell lines
are freely available to researchers.
254 All MGD resources
are freely available to the research community.
255 All mutant fish
are freely available to the scientific community through
256 MGD resources
are freely available to the scientific community.
257 For millennia, seeds have
been freely available to use for farming and plant breed
258 LIGSIFT software, including the source code,
is freely available to academic users at http://cssb.bio
259 part of Pathway Tools (version 17.5), which
is freely available to academic users, and for a fee to
260 Pathway Tools software
is freely available to academic users, and for a fee to
261 The ZDOCK server
is freely available to all academic and non-profit users
262 ion module of the Sfold RNA package, STarMir
is freely available to all at http://sfold.wadsworth.org
263 The ModFOLD4 server
is freely available to all at: http://www.reading.ac.uk/
264 This web site
is freely available to all users and there is no login r
265 Tra v2.0 has an intuitive user interface and
is freely available to all users without any login requi
266 The server
is freely available to all users without restriction.
267 STITCHER 2.0
is freely available to all users without signup or login
268 The database
is freely available to download from the ftp site: ftp:/
269 Our eQTL database based on these results
is freely available to help define the function of disea
270 lementation of our user-oriented web crawler
is freely available to non-commercial users via the foll
271 The Java implementation of the algorithm
is freely available to noncommercial users.
272 NMRbox
is freely available to not-for-profit users.
273 The AGRP
is freely available to researchers through an imputation
274 The toolbox
is freely available to the community under an open-sourc
275 This tool
is freely available to the research community and can be
276 mpatible software package, MendelScan, which
is freely available to the research community.
277 implemented in software called ReXpress and
are freely available,
together with source code, at http
278 assembly tools except CLC Genomics Workbench
are freely available under GNU General Public License.
279 Its implementation
is freely available under a 2-clause BSD license, with b
280 d at http://rest.ensembl.org and source code
is freely available under an Apache 2.0 license from htt
281 The code
is freely available under Apache 2.0 license at www.gith
282 , along with a set of pre-compiled binaries,
is freely available under GNU General Public License fro
283 The source code for ICMA
is freely available under MPL 1.1 or GPL 2.0 or LGPL 2.1
284 Circleator
is freely available under the Artistic License 2.0 from
285 This R package
is freely available under the Gnu Public License (GPL-3)
286 ge, with detailed instructions and examples,
is freely available under the GPL (> = 2) license from t
287 The package
is freely available under the GPLv3 license through Bioc
288 The source code
is freely available under the MIT license at https://mgy
289 The package
is freely available under the MIT license from CRAN.
290 GE (Scoring function for Assembled GEnomes),
is freely available upon request.
291 empirical Bayesian algorithms in this paper
is freely available upon request.
292 The benchmark data and software
are freely available via two R/Bioconductor packages, mi
293 ntation is available online, and source code
is freely available via GitHub.
294 The code
is freely available via http://gtfold.sourceforge.net/pr
295 dependencies as a pre-configured system, and
is freely available via the installation instructions pr
296 BISQUE
is freely available via the web using any major web brow
297 Data
are freely available without restriction.
298 otification, provided example submission and
is freely available without any registration requirement
299 LASAGNA-Search 2.0
is freely available without registration at http://biogr
300 CCBuilder
is freely available,
without registration, at http://coi