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1 Registry, and the bundled-payment enrollment file.

2 EST output files can be merged into a single file.

3 that is superior to that using the original file.

4 ional results are included in a supplemental file.

5 red from the 100% FFS Part B Medicare Claims File.

6 the Physician and Other Supplier Public Use File.

7 (iv) unaligned protein sequences in a single file.

8 me needed for data treatment from 20 to 5min/file.

9 obtained from the 2010 Area Health Resource File.

10 data are in the form of a tab-separated text file.

11 y at least two individuals walking in single file.

12 ful queries without decompressing the entire file.

13 sign is digitally built as a detailed 3D CAD file.

14 a binding intensity file (bigWig) or a peak file.

15 ity Improvement Program 2012 Participant Use File.

16 harts for all isotopologues, and a .csv data file.

17 th length across epidermal atrichoblast cell files.

18 oped that perform diverse analyses using VCF files.

19 lysis of the variant data within VCF and BCF files.

20 ta file stubs from raw XML metabolomics data files.

21 dentify and parameterize APs from text input files.

22 R-STAR version 2.1 and version 3.1 formatted files.

23 compared with the htslib C library using BCF files.

24 for Medicare and Medicaid Services research files.

25 fast alignment algorithm that generates SAM files.

26 ing sample identities from FASTQ, BAM or VCF files.

27 d the complexities of using error prone flat-files.

28 rectly from an MRI scanner, or from raw data files.

29 om the Medicare Provider Analysis and Review files.

30 nformation from these large and complex data files.

31 ol for use with BAM, CRAM and SAM sequencing files.

32 i-line sequences, whilst identifying invalid files.

33 erator reaction arrows are now input in text files.

34 using the Medicare Inpatient and Denominator files.

35 ST API or downloadable as tab-delimited text files.

36 stimated by using unit costs from 2 national files.

37 idth direction increasing the number of cell files.

38 files and their equivalent JSONized NMR-STAR files.

39 tasks with just a single pass over the data files.

40 pulation (n = 16,340) using driver's license files.

41 03, 2006, and 2009 Hospital Market Structure files.

42 inked birth certificates and hospitalization files.

43 also accepts simple text or comma delimited files.

44 een NMR-STAR and JSONized NMR-STAR formatted files.

45 g Medicare and California hospital discharge files (1993-2012) and self-completed questionnaires.

46 ructed from Medicare National Claims History files (2002-2006), including 28 million Medicare benefic

47 ad some of the anaphylaxis ICD-10 codes; 309 files (46%) from 209 patients had anaphylaxis and allerg

48 oarray platforms), alongside 17 RNA-Seq data files (7 SCN and 10 WB).

49 ed consent) who underwent spinal surgery and filed a malpractice claim were studied (mean [SD] age, 4

50 Given a PDB file (a Protein Data Bank file format containing the 3D

51 Pymol scripts together with PDB files allow movies of individual Q- and R-cPCA modes to

52 rameters are embedded in instrument raw data files, an opportunity exists to capture this metadata mo

53 For each file analyzed our software generates a summary of the qu

54 As input, BRAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of

55 PARTIE subsamples reads from the sequencing file and calculates four different statistics: k -mer fr

56 xamine an Illumina genotyping array manifest file and can detect all problematic SNPs, including SNPs

57 care Physician and Other Supplier Public Use File and did not constitute human subject research.

58 ng Standard Transplant Analysis and Research file and divided into 3 equal eras based on the date of

59 The website also contains a README file and other relevant instructions for running the cod

60 pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BI

61 Medicare Part D 2013 prescriber public use file and summary file were used to calculate medication

62 ata: Physician and Other Supplier Public Use File and the CMS-sponsored August through December 2013

63 icare Physician and Other Supplier aggregate file and the Physician and Other Supplier Public Use Fil

64 error-correct and assemble reads from a CRAM file and then align with BWA-MEM.

65 , (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single f

66 ing and manipulating data stored in NMR-STAR files and as a command-line tool to convert from NMR-STA

67 brary (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Pho

68 he MIT License and is accompanied by example files and data.

69 eumonia using the Medicare Standard Analytic Files and Enrollment Database together with VA administr

70 re packages require specific formatted input files and generate output files in various types, yieldi

71 from a national IHCA registry with Medicare files and identified 36 961 patients >/=65 years of age

72 for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility.

73 Federal Area Health Resources Files and Medicare 5% research identifiable files were u

74 DEGs, capacity to directly process alignment files and methods for testing differential APA usage.

75 changes in the numbers of longitudinal cell files and of cells along the leaf length.

76 Among these patients, the files and operational notes of eight patients who underw

77 ted novel tools that analyze or annotate VCF files and organized these tools into a command-line base

78 We also reviewed our own files and reference lists of articles identified by this

79 ing because of the increasingly complex data files and studies with a greater number of samples.

80 ts, some material was moved to supplementary files and the regression was performed without variable

81 can read, edit, and write NMR-STAR formatted files and their equivalent JSONized NMR-STAR files.

82 examine the relationship between bankruptcy filing and survival.

83 the data sets, data dictionary, case report file, and statistical analysis plan from the original tr

84 agonal (R-T) phase transition under electric-filed, and is recoverable from tetragonal-rhombohedral (

85 ty to submit methylation and BioNano mapping files, and a database of anti-microbial resistance genes

86 ent as publishable figures, as standard data files, and as linked data, including bulk and programmat

87 was used for joint calling of 180 TB of BAM files, and ORNL and Rice supercomputers were used for th

88 imes faster than PLINK v1.9 with VCF and BCF files, and over 16 times faster than vcftools.

89 data processing, from sra-fastq files to bed files; and unifies the processing of multiple replicates

90 Though the field agrees that smaller files are advantageous, the cost of lossy compression, i

91 However, VCF files are large and data retrieval is relatively slow.

92 In monocot leaves, stomatal cell files are positioned at the flanks of underlying longitu

93 InterVar can take a pre-annotated or VCF file as input and generate automated interpretation on 1

94 that takes next-generation sequencing fastq files as input, calls on several well-established and fr

95 on using a peak-picker-output and MS(2) data files as inputs.

96 h takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis

97 primarily maintained and accessed in a flat file ASCII format known as NMR-STAR.

98 -driven repository that hosts digital design files, assembly specifications, and open-source software

99 identifiers have been left off the research files because they could compromise the confidentiality

100 ein or that specification is induced in cell files beyond the vein.

101 ic dataset, for example, a binding intensity file (bigWig) or a peak file.

102 re that facilitates quality control of FASTQ files by carrying out a QC protocol using FastQC, parsin

103 whole transcriptome shotgun sequencing data files by trimming reads and removing adapters, mapping r

104 The atlas and associated files can also be used for planning stereotaxic surgery

105 PyMOL session files can be downloaded, allowing high-quality publicati

106 tenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file.

107 r structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorp

108 The simulation system and input files can be used for CHARMM, NAMD, GROMACS, AMBER, GENE

109 CNTPs), which confine water down to a single-file chain, exceeds that of biological water transporter

110 pidly and reversibly reorganized into single-file chain-like geometries that substantially reduced th

111 The files clinically validated as being anaphylaxis were man

112 he gap between theoretical and practical WIG file compression rates.

113 ts are built around a unique and centralized file containing sample names, replicates, conditions, an

114 plify the reading of Protein Data Bank (PDB) files containing glycans through the automatic detection

115 Cellerator arrow notation from standard text files, conversion to differential equations, generating

116 reconstruction, with network and annotation files created for visualization in Cytoscape.

117 andomized to the binocular game and with log file data available performed more than 75% of the presc

118 and analyzing raw next generation sequencing files derived from pooled screening experiments while at

119 Unfortunately, current PDB files do not provide exact annotations for most carbohyd

120 Variant call format (VCF) files document the genetic variation observed after DNA

121 by analysing all the consecutive inpatients' files documented as allergies from the University Hospit

122 n any web browser, improved support for data file download and enhanced organization of website pages

123 rs for Medicare and Medicaid Services annual files, downloaded from the Hospital Compare website.

124 publication bias shifted from worrying about file-drawered studies to worrying about p-hacked analyse

125 , and compatible with common genotype format files (e.g. PLINK and vcf).

126 The website takes as input two files, each of which can be in either PDB or mmCIF forma

127 n bootstraping) of short-reads based on SAM files facilitating the investigation of sequencing depth

128 gram Colectomy Targeted Participant Use Data File for 2012 and 2013.

129 ts a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S

130 Patients with cancer are more likely to file for bankruptcy than the general population, but the

131 factors between patients who did and did not file for bankruptcy, we then fit Cox proportional hazard

132 0 drugs or genes, but the output is an Excel file for each drug or gene.

133 tes and readily accepts a shareable 'recipe' file for each run to either replicate previous results o

134 redictions are provided in the supplementary file for further biomedical research.

135 I networks are provided in the supplementary file for further biomedical research.

136 Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped ser

137 Patients who filed for bankruptcy (n = 4,728) were more likely to be

138 for mortality among patients with cancer who filed for bankruptcy versus those who did not was 1.79 (

139 s' period linked birth/infant death data set files for 2007-2013 for 26546503 US births through June

140 rvices Medicare Part D Prescriber Public Use Files for 2013, 2014, and 2015 were accessed.

141 erating ensembles of electrostatic potential files for a library of mutants to quantify the effects o

142 ent-free module can be run directly on FASTQ files for a quick initial check.

143 Medicare Part B National Summary Data Files for calendar years 2000 to 2014 were used to ident

144 machine-readable network data and public use files for individual federal exchange plans from the Cen

145 generate grid-based electrostatic potential files for protein structures provided by the end user.

146 and users are only required to submit FASTA files for their genomes and genes of interest.

147 IGG marker files for three sets of genomes, Solanum lycopersicum/So

148 R, 2.1; 95% CI, 1.1 to 4.0); and thoughts of filing for bankruptcy (OR, 6.6; 95% CI, 3.0 to 14.3).

149 (1) borrowing money or going into debt, (2) filing for bankruptcy, (3) being unable to cover one's s

150 cing data are becoming prevalent, a standard file format and tools for working with these data conven

151 MR-STAR file format into its equivalent JSON file format and vice versa, and to visualize chemical sh

152 Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein

153 ress this problem, we propose a standardized file format for representing V(D)J analysis results.

154 tform- and language-independent hierarchical file format for which user-friendly viewers are availabl

155 a command-line tool to convert from NMR-STAR file format into its equivalent JSON file format and vic

156 The VDJML file format specification is accompanied by a support li

157 ipation from the community in developing the file format standard, as well as code contributions.

158 The PDB archive is available in MMTF file format through web services and data that are updat

159 ftware tools produces results in a different file format, and can annotate the same result using diff

160 Its outputs are visual, textual and PDB file format.

161 nd Python, for reading and writing the VDJML file format.

162 ndardized files into software-specific input file formats as well as standardize and summarize infere

163 oton-HDF5 files and convert several existing file formats into Photon-HDF5.

164 omprehensive variant annotation with diverse file formats is difficult with existing methods.

165 ain priorities: the development of tools and file formats to support segmentation (that is, the decom

166 cerDMRI supports clinical DICOM and research file formats, is open-source and cross-platform, and can

167 ned for datasets in new and rapidly evolving file formats, which may lack extensive software support.

168 y plots may then be produced in a variety of file formats.

169 n and supports genomics datasets in standard file formats.

170 ergence of many new methods and a variety of file formats.

171 Patient files from 26 trials run by 18 trial groups were reviewe

172 s were linked to statewide birth certificate files from January 2000 to December 2014 to identify pos

173 2, 2008, through April 16, 2015; the merged files from these data were created between June 5, 2015,

174 flowAI, containing two methods to clean FCM files from unwanted events: (i) an automatic method that

175 currently no standardized format for output files from V(D)J analysis.

176 alysis of the 100% Medicare inpatient claims file, from January 1, 2008, to November 30, 2011, and ma

177 r and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices

178 and labels, which are specified in a config file generated by the first run of Synima - and can be s

179 The algorithm reads the SAM files generated by the alignment algorithms using multip

180 nd real- (floating point) valued RNA-seq WIG files generated by the ENCODE project.

181 and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence

182 cilitate this effort, compression of genomic files has been proposed.

183 er that allows access to metagenome analysis files hosted on a server, we provide a straightforward,

184 Quality Improvement Program Participant Use File identified 12 variables independently associated wi

185 our major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (ii

186 iles, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files

187 and conversion of Variant Call Format (VCF) files; (iii) detection of linkage, i.e. construction of

188 ndom querying of a subregion from a BAM-like file in an encrypted form.

189 RAKER1 requires a genome assembly file and a file in bam-format with spliced alignments of RNA-Seq re

190 udes an alignment in FASTA format and a tree file in newick format.

191 ted pKa values and provides the downloadable file in PQR format.

192 Prospective analysis of data on file in surgical cases between January 2007 and December

193 a post-processing step to existing alignment files in BAM format.

194 tches of data with tools designed to process files in bulk.

195 ract static images and machine-readable data files in PDB format from the multi-scale structure.

196 tures, particularly across thousands of data files in population scale experiments.

197 home page for basic use, requiring only two files in Protein Data Bank (PDB) format.

198 e provides code examples to read Photon-HDF5 files in several programming languages and a reference P

199 luding a comprehensive parts list, 3D design files in STEP (Standard for the Exchange of Product mode

200 ustomizable input modes, and it outputs data files in text and PDF formats.

201 and it allows for fast selection of relevant files in the compressed domain via maintenance of taxono

202 hanisms and optimal path to move each of the files in the manifest to the site of workflow execution.

203 ic formatted input files and generate output files in various types, yielding practical inconvenience

204 The DSSR web service accepts 3D coordinate files (in mmCIF or PDB format) initiated from a Jmol or

205 These files include geographic information at the county level

206 The merged file included data for all male adolescents who visited

207 sential utilities to process and analyze VCF files, including primer generation for variant validatio

208 that can process the full set of valid FASTQ files, including those with multi-line sequences, whilst

209 genome-wide epigenomics data from sequencing files into a final report, built with a comprehensive se

210 ics, diagnoses, and costs from SEER-Medicare files into a person-year panel data set.

211 olkit (LAIT), which can convert standardized files into software-specific input file formats as well

212 The file is then loaded into an online web application that

213 developed fqtools; a fast and reliable FASTQ file manipulation suite that can process the full set of

214 These include reliance on file modification times to determine whether a target is

215 was randomly selected from birth certificate files (n = 12990) with frequency matching on maternal ag

216 energy definitions, in order to produce the files necessary to use SBMs with high performance molecu

217 ng Standard Transplant Analysis and Research-file of adult LTs from 2002 to 2014.

218 The input file of MMiRNA-Viewer contains the expression informatio

219 e function values is possible with a summary file of ranked solutions.

220 d any query result, including a downloadable file of the full database with additional variant detail

221 The files of 107 patients (136 eyes) on whom surgery was per

222 y datasets, stored in an arbitrary number of files of any size.

223 y, and End Results Program releases research files of cancer registry data.

224 divisions give rise to patterns of parallel files of cells, the genetic basis of which remains uncle

225 Alternatively, the GFF files of several model organisms have been pre-loaded so

226 IIM model can be found in the supplementary files of this article.

227 can also be used to browse local annotation files offline and to generate high-resolution figures fo

228 text]3 min to process a 30x whole-genome BAM file on a desktop computer.

229 an priority patent n degrees 102015000084813 filed on 17th December 2015) on wheat kernel endosperm m

230 eely available to accessors either as single files or as complete data bank downloads.

231 imiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-

232 both NMR-STAR version 2.1 and 3.1 formatted files, parsing them into usable Python dictionary- and l

233 omputer scientists study the distribution of files per directory.

234 UClncR takes standard RNA-seq alignment file, performs transcript assembly, predicts lncRNA cand

235 -alone pipeline that includes sequencing BAM file post-processing, joint segmentation of total- and a

236 These result files provide greater control and insight during experim

237 Critical Intermediate calculation files provided as Tables S3 and S4.

238 hon libraries for parsing NMR-STAR formatted files: PyStarLib, NMRPyStar, and PyNMRSTAR.

239 From all 2318 files related to allergic or hypersensitivity conditions

240 Deposition of files requires free user registration.

241 lity of these data (in FASTQ or SAM/BAM/CRAM files), resulting in compression ratios that significant

242 Wing cell files reveal an anisotropic growth pattern, and computat

243 y other than distributing the code through a file sharing service.

244 faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF.

245 time of the IMS experiment and the resulting file size.

246 pe information into vectors that allow small file sizes and operational transformations.

247 chmarks using 1000 Genomes Phase 3 data show file sizes are 14.0 Gb (VCF), 12.3 Gb (BCF, binary VCF),

248 On average, the compressed file sizes were 2-13 percent of the original raw metagen

249 ommunities and hence tend to result in large file sizes, typically ranging between 1-10 GB.

250 ferring fine details at the expense of large file sizes, whereas vector graphics encrypts shape infor

251 2-13 percent of the original raw metagenomic file sizes.

252 This article details a file standard and novel software tool suite for working

253 We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the acc

254 single locus NGS data, there is currently no file standard or analysis tool suite for manipulating an

255 ecific sequences, format conversion or basic file statistics).

256 can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files.

257 Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to tr

258 from the classification of organisms to the file system on a computer.

259 ancer Society, has created a shared research file that has changed the study of cancer care in the Un

260 are easily set using a single configuration file that provides centralized tracking of all analytica

261 monly used SBMs, and it can process template files that are altered according to the needs of each us

262 n on networks and disk arrays, create output files that are minimal in size, and run in a highly comp

263 built with a comprehensive set of annotated files that are navigated through a graphic user interfac

264 By converting the 1KG data into files that can be imported into popular pre-existing too

265 MOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process

266 lity, we introduce cartographical snapshots: files that describe a particular map and visualization s

267 on of several Jupyter notebook demonstration files that enhance reproducibility and provide the capab

268 hmic parameters, and returns multiple result files that include a facility for the user to draw their

269 JED output results as text files that include transformed coordinates for aligned s

270 On the tested files, the memory usage of the algorithm never exceeded

271 ns, the construction of auxiliary restraints files, the selection of the energy parameters, and the a

272 ry levels of data processing, from sra-fastq files to bed files; and unifies the processing of multip

273 o compress and stream recently acquired data files to data processing servers, mimicking just-in-time

274 sequencing data, we processed mapping (BAM) files to extract coverage, representing log R ratio (LRR

275 sets, utilizes human-readable configuration files to manipulate the pages and tabs, and is extensibl

276 2013 were linked to fee-for-service Medicare files to obtain 30-day mortality.

277 System (UMLS) knowledge sources to map text files to standard biomedical concepts.

278 While many file types and analysis tools exist for storing and mani

279 Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional

280 of this data, it was placed into a computer file using an individual identifying numbers for each in

281 of this data, it was placed into a computer file using an individual identifying numbers for each in

282 tion distortion; (iv) data imputation on VCF files using a new approach, called LB-Impute.

283 the large size of human genome sequence data files (varying from 30 GB to 200 GB depending on coverag

284 METHODS AND Using statewide hospitalization files, we identified discharges for acute myocardial inf

285 From the ACS-NSQIP 2011-2012 patient user files, we selected core emergency surgical cases also co

286 Using Medicare Provider and Analysis Review files, we studied patients from age 65 to 100 years who

287 Using Medicare Provider and Analysis Review files, we studied patients from age 65 to 100 years who

288 2013 prescriber public use file and summary file were used to calculate medication costs by physicia

289 Once validated, Lake Michigan trout data files were analyzed for polyfluoroalkyl acids using the

290 rum samples and data extraction from patient files were conducted from December 2016 through February

291 potential silencing of OsSHR2, stomatal cell files were observed both in the normal position and in m

292 Audio files were transcribed, translated into English and recu

293 Files and Medicare 5% research identifiable files were used to compute parameters related to the rad

294 State hospitalization files were used to identify all patients with an acute m

295 e. Spliceman now accepts variant call format files), which allow much larger inputs than previously a

296 of the Medicare Part D Prescriber Public Use File, which details annual drug utilization and spending

297 ed features are organized in structured data files, which are easily parsed with any programming lang

298 rate and export this nucleus model to a text file with a specific format that can be read by Geant4 u

299 computer operating system, movie, and other files with a total of 2.14 x 10(6) bytes in DNA oligonuc

300 (ii) Users may upload sequence files with reads representing unknown taxa and place the