ライフサイエンスコーパス: file

1 ned data from the 2017 Area Health Resources File.

2 of the location, format or structure of the file.

3 r a given interval in a bedGraph or a bigWig file.

4 ondary xylem zone with less xylem cells/cell file.

5 and, utilizing graphviz to generate an image file.

6 y visualize a pedigree given a pedigree text file.

7 s the information back from DNA to a digital file.

8 ents from the Multiple Cause of Death (MCOD) file.

9 led via a single user-friendly configuration file.

10 increasingly assigning additional cores per file.

11 n align reads to a BLAST database or a FASTA file.

12 hATE are included in the distribution README file.

13 ying the desired analyses in a configuration file.

14 Quality Improvement Program Participant Use File.

15 as they dominate the size of the compressed file.

16 ion numbers found in the variant-centric XML file.

17 ough the size of the compressed network data file.

18 weight distributions of the 2017 US Natality file.

19 vided as either JSON or a tab-separated text file.

20 The DICOM images were converted to STL files.

21 ess to large amounts of genomic data as flat files.

22 eric and typed handling of CIF and BinaryCIF files.

23 ssion by linking hospital records with death files.

24 package with easily-handled input and output files.

25 information on genomic variants in input VCF files.

26 vel variant-based index for querying VCF/BCF files.

27 and concisely summarizes statistics from VCF files.

28 These data are mostly stored as VCF-format files.

29 computational cost of reading text-based PDB files.

30 ther analyse single variants or complete VCF files.

31 Sanger imputation servers), IMPUTE2 or PLINK files.

32 ring the import of transcript quantification files.

33 ially designed for nanopore sequencing FASTQ files.

34 ted from customized child contact management files.

35 neous queries on both the GFF and expression files.

36 m is the use of incomplete genome annotation files.

37 achines, and tables can be downloaded as CSV files.

38 notations are all available as Supplementary Files.

39 er retrieval but doubles the size of the GFF files.

40 resentations, sometimes referred to as event files.

41 n a factor of two versus gzip compressed CIF files.

42 y identified by any known powder diffraction files.

43 pect of mRNA drug development and regulatory filing.

44 Supplementary File 1 contains Supplementary Table 1, Supplementary Fig

45 he following website *contains Supplementary File 1 material and the code.

46 eal data analysis is available as Additional file 1.

47 two groups (39.4% versus 29.6%) (Additional file 1: Table S1).

48 lclock times, are available in Supplementary Files 1, 2 and 3.

49 27%, p = 0.002) and AD inclusion in hospital files (10% versus 3%, p < 0.001) were more likely in the

50 d 20-90 from the NHANES III Linked Mortality File (1988-1994).

51 Supplementary File 2 contains Supplementary Tables 2-6 and 8.

52 onal Center for Health Statistics Birth Data Files (2011-2016), difference-in-differences (DID) and d

53 Supplementary File 3 contains Supplementary Table 7.

54 The updated Additional file 5 is published in this correction.

55 [1], the authors submitted a new Additional file 5 to replace the one containing formatting issues.

56 flow signals occupy a big portion of the BAM file (about 75% for the human genome).

57 ional burden in designing sets of orthogonal file addresses.

58 rat, and human brain flatmap vector graphics files (Adobe Reader/Acrobat viewable and Adobe Illustrat

59 ims in the United States, 4081 closed claims filed against general surgeons from 1995 to 2015 were re

60 ults of analysis were presented in browsable files along with a variety of visualization options.

61 platforms with automatic synchronization of files among isolated file systems.

62 truct split reads given a sequencing summary file and alignment to a reference.

63 Oligo commences when a user uploads an input file and concludes with the generation of a result-set c

64 minated practice leads to interpret the data file and implement guideline-based patient-level CKD man

65 The BulkVis tool can load a bulk FAST5 file and overlays MinKNOW (the software that controls ON

66 user to specify the target protein as a PDB file and the ligand as a SMILES string.

67 from the apical third of roots using a #10 K file and then amplified using multiple displacement ampl

68 ires users to download/install an executable file and to run that file from a command-line interface.

69 2015 Physician Compare National Downloadable file and US Census data.

70 ic Mutual Insurance Company from closed case files and by the New York State Health Department from t

71 Taking bam/sam files and cell cluster labels as inputs, scDAPA detects

72 ser cutter, starting from open-source design files and commercially available components.

73 ense version 3 and is accompanied by example files and data.

74 ts' clinical data were obtained from medical files and each infant was assigned a clinical severity s

75 ols is a suite of tools for working with BUS files and facilitates rapid quantification and analysis

76 r compression-factor ten and four versus CIF files and gzipped CIF files, respectively.

77 udy cases were identified from institutional files and included COVID-19 (n=15: 12 active, 3 cleared)

78 upload and download spatial datasets, store files and link to the ALA spatial portal, improve graphi

79 mulation inputs and outputs via standardized files and provides much flexibility for adding new conve

80 tomization is possible through configuration files and Python API.

81 ory approach, and regulatory process for NDA filing and approval.

82 marized in HTML web page, tab-delimited text file, and high-resolution image formats.

83 s that explain how to prepare model and data files, and how to use the software SBMLsimulator in comb

84 Energy measurements, the scanners' log files, and the radiology information system from the ent

85 sion of advance directives (ADs) in hospital files, and use of hospital care.

86 ion is encoded, databases are organized, and files are accessed.

87 Such files are in a bedGraph text format or a bigWig binary f

88 nthesized libraries of Ugi products, and the files are read back using mass spectrometry.

89 When files are shared publicly or among collaborators with in

90 Variant call format (VCF) files are the standard format for representing variant d

91 Pedigree files are ubiquitously used within bioinformatics and ge

92 redictor by far, for the Republican rank-and-file as a whole and for a variety of subgroups defined b

93 CBI data or can accept user's private bigwig files as input to plot the concerned data on promoters,

94 to take both nucleotide and protein sequence files as inputs, and output a result page with graphic r

95 t formats such as binary output, wig and bed files as well as csv files to export the location of all

96 ysis workflow, intermediate input and output files, as well as alternative reanalyses of the same dat

97 Detailed design files, assembly instructions and control software are pr

98 ulates a parameter database in each task and file associated with a pipeline stage, JUDI simplifies p

99 Long Ranger, generates the essential output files (BAM, VCF, SV BEDPE) necessary for downstream anal

100 s are found to preferentially flow in single-file, branched chains within the POCs.

101 practices (11,706 patients) received a data file but otherwise, continued usual CKD care.

102 hree anesthesia-related claims or suits were filed by 50 plaintiffs.

103 Of all ERPOs, 87% were filed by law enforcement and 81% were granted.

104 lication for conveniently validating mzTab-M files by a graphical user interface, and a command line

105 er the pairwise comparisons within the input files by fold change direction (sign).

106 base search process of raw mass spectrometry files by including an in-house built database of mutated

107 ion in the quality storage portion of a CRAM file can be achieved while maintaining variant calling a

108 online access), departments from which cine files can be requested, fees, and processing times.

109 a minimal setup CLI and API, FASTQ support, file chunking for large sequence files, JSON and Python

110 erialization of Crystallographic Information File (CIF) format files that maintains full compatibilit

111 rics LifeLink) that included persons who had filed claims between 2006 and 2015 in the United States.

112 ing of only 40 cylindrical cells in a single-file column.

113 provided to enable users to download the SQL file, computational structural features and PTM sites' d

114 ulk of space taken up by NGS sequencing CRAM files consists of per-base quality values.

115 and negative controls and test MRSA sequence files contained <0.14% and <0.48% of fragments that matc

116 In our experiments, we store a file containing sheet music of Mozart, and show perfect

117 aires, standard case forms, and digital case files containing characteristics of individuals were use

118 e list mode, A-Lister accepts delimited text files containing lists of names as input.

119 The system can accept files containing millions of variants and handle single-

120 Nanopore sequencers output FAST5 files containing signal data subsequently base called to

121 We generate files containing the figures and their associated captio

122 A separate file contains an instance-level prototype in OWL that de

123 We introduce FluoroMatch, which automates file conversion, chromatographic peak picking, blank fea

124 from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for

125 d medicinal chemistry strategy of deliberate file enrichment around molecules bearing the hallmarks o

126 particle focusing to align cells in a single file for improving sorting accuracy and efficiency witho

127 and the amount of memory to be allocated per file for optimum performance.

128 Here, we introduce a new wetland forcing file for the ORCHILEAK model, which improves the represe

129 The ERPOs were filed for concerns about harm to self (n = 67), harm to

130 rvices Medicare Part D Prescriber Public Use Files for 2013, 2014, 2015, and 2016 were accessed.

131 ron microscopy (EM) density maps, and export files for 3D printing.

132 well as DHS and ATAC-seq that yield coverage files for chromatin accessibility.

133 o improve the compression of the Ion Torrent files for long term archiving.

134 compression tool to compress Ion Torrent BAM files for long term archiving.

135 on of quality metrics for sequence alignment files for multiple experiments generated by Cell Ranger

136 tional Center for Health Statistics natality files for the years 2011-2017.

137 ChIP-seq and ChIA-PET that generate coverage files for transcription factor binding, as well as DHS a

138 Leveraging the SONATA file format and existing software such as NEURON, NEST,

139 We developed a file format called cooler, based on a sparse data model,

140 e ecosystem including a new efficient binary file format named 'ribo'.

141 s implementation is a json syntax-compatible file format, which can capture detailed metadata for all

142 owser supports visualizing a large number of file formats for genome annotation, variant calling, rea

143 y information in programmatically accessible file formats tailored for machine learning frameworks.

144 Structural biology relies on specific file formats to convey information about macromolecular

145 ciency and comprehensive support for popular file formats will facilitate method development, softwar

146 e scales, integrating genomes from different file formats, performing required filtering, stitching d

147 ity to read mass spectral data from standard file formats, process it, and visualize it.

148 manipulating and saving PDB, mmCIF and MMTF file formats.

149 stimation of paired tumor-normal VCF variant file formats.

150 ement Program Pediatric Participant Use Data File from 2013 to 2017.

151 d/install an executable file and to run that file from a command-line interface.

152 The Part B National Summary Data Files from 2007 to 2017 were obtained through the Center

153 can also incorporate and compress expression files from both bulk and single-cell RNA-Seq experiments

154 ristics of a study and easily decrypting the files from dbGaP.

155 ctionality for importing data tables and xml files from HPA, exporting and visualizing data, as well

156 rvices 100% inpatient Limited Data Set (LDS) files from January 2013 through September 2015 to calcul

157 eq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMast

158 Researchers often download a subset of data files from these repositories to perform exploratory dat

159 using high-resolution mass spectrometry data files generated by an atmospheric pressure gas chromatog

160 ) file (we consider training and testing VCF files generated with the same tools, as we assume they w

161 n packages (e.g., Nilearn, Scikit-learn) for file handling, visualization, and machine learning.

162 We also show that memory allocation per file has a lower priority in performance when compared t

163 The Supplementary Information file has now been updated to include the corrected Figur

164 All other supplementary files have now been updated accordingly.

165 s with a simple interface to upload an input file in BED format and customize parameters for each tas

166 r the models used in this paper are in a zip file in the supplementary material.

167 Users can save the generated image file in various formats.

168 erformed CNV discovery from the original BAM files in 292 min using 640 executor cores on a Spark clu

169 propose GPress, a framework for querying GFF files in a compressed form.

170 tein sequences for genomic variants from VCF files in a user-friendly and efficient manner.

171 m implements several modules to manage large files in an easy and efficient way.

172 ies of parallel venation and linear stomatal files in monocots, and the reticulate patterning of vein

173 Data were extracted from software log files in the Lights On Network (Cerner) during 2018 that

174 oped interfaces for writing and reading ribo files in the R (RiboR) and Python (RiboPy) environments.

175 publication to add links to the Peer Review file.In addition, affiliations 16 and 17 incorrectly rea

176 he usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data.

177 it accessible to users who have knowledge of file input/output and matrix manipulation in R and a mod

178 e use Pyrococcus furiosus Argonaute to punch files into the PCR products of Escherichia coli genomic

179 For the BAM files, IonCRAM could achieve a space saving of about 43%

180 The correct additional file is given below.

181 Moreover, the decryption of the files is a complex procedure.

182 While the text based format of ped files is efficient for computational methods, it is not

183 er, generating summary statistics from these files is not always straightforward.

184 ing Python package for operating on coverage files is not optimized for speed.

185 TQ support, file chunking for large sequence files, JSON and Python dictionary output, and built-in s

186 Existing utilities for accessing these files, like gffutils and gffread, do not focus on reduci

187 d expression in dysplastic glands and indian file-like cells infiltrating adipose tissue.

188 amic focusing drives cells along in a single file line, keeping the cells from clumping and thus ensu

189 care setting and not captured in membership files may have been missed.

190 53,848 annotation (GFF) and assembly (FASTA) file metadata.

191 notch nanogrooves confined them into single-file molecular chains.

192 The collective "single-file" motion of water molecules through natural and arti

193 , de novo sequencing results, proteogenomics files, MS/MS data in mzML/mzXML format and data from pub

194 for local or remotely hosted indexed genomic files, not only for visualization but also data transfor

195 rs results in strongly reduced vascular cell file numbers, whereas ectopic expression of both TMO5 an

196 tabilization based on laboratory and limited filed observation.

197 rogram designed for the study created a data file of patients with CKD in participating practices.

198 dataset in BAM format and a pre-compiled VCF-file of targeted clinically relevant variants it associa

199 les the nonmarginal, radially arranged tooth files of arthrodires, an early group of armoured fishes.

200 We tested GPress on several GFF files of different organisms, and showed that it achieve

201 We used CaSQ to produce executable files of existing molecular maps that differ in size, co

202 palliative care and AD inclusion in hospital files of intervention patients is meaningful and require

203 as new tooth positions are inserted into the files of sequential addition when a gap appears.

204 he bony plate are aligned with the alternate files of teeth, whereas new tooth positions are inserted

205 carcinomas were identified in pathology case files of the Massachusetts General Hospital/Massachusett

206 (from DNA extraction to availability of data files) of 24 hours.

207 Data were collected from patients' files on hospitalised patients with a diagnosis of cUTI

208 s well as implementing a range of in-storage file operations.

209 quires two unmasked half-maps and a sequence file or other source of information on the volume of the

210 MM achievement measured variously as patents filed or licensed, companies founded, number of papers a

211 in tabular form and in graphical form as SVG files or in data format as JSON or csv.

212 and annotations, provided by local tools and files or via ReST APIs, and classifies variants accordin

213 rmalization strategies: normalizing samples (files) or normalizing features (genes).

214 the version of the Supplementary Information file originally published with this Article, the images

215 A PyMOL file, PDB file, PDB identifier code or protein/gene name

216 A PyMOL file, PDB file, PDB identifier code or protein/gene name can be pr

217 The file qcSSMDhomo_1.0.0.tar.gz (for Windows) containing qc

218 ave been chosen, the package produces output files ready for MCMCtree analysis.

219 Here, we demonstrate reliable file recovery with PCR-based random access when as few a

220 rates the mutant structure and configuration files required to execute molecular dynamics simulations

221 sources, because the data is stored in large files, requiring large bandwidth to download and special

222 en and four versus CIF files and gzipped CIF files, respectively.

223 , larger cortical cells, fewer cortical cell files), restrict uptake of water to conserve soil moistu

224 e size and sequencing coverage on successful file retrieval and look for systematic DNA strand drop o

225 When tested on entire files retrieved from the MassIVE repository, MassComp ac

226 l/ring infiltrate was associated with single-file round/ovoid objects (OR 7.78; 95% CI, 2.69-22.35, P

227 Absence of single-file round/ovoid objects was associated with a BCVA of 6

228 s can specify thresholds to filter the input file(s) by column(s) such as p-value, q-value, and fold

229 e Inpatient and Outpatient Standard Analytic Files (SAFs) from years 2012 to 2016.

230 g on the non-quality content of the original file (see Supplementary Material S6 for details).

231 We demonstrate the File Server in two use cases: (i) integration with Galax

232 The File Server library decouples data retrieval and transfo

233 We developed Epiviz File Server, a Python library that implements an in situ

234 nerated by GPress instead of to the original file shows a size reduction of more than 44% on average.

235 ction in both mean number of images and mean file size (P < .001 for both).

236 Finally, we also investigate the effects of file size and sequencing coverage on successful file ret

237 schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip comp

238 Ribo files store all essential data grouped by ribosome footp

239 pload or processed in real-time via links to files stored remotely on an FTP repository.

240 ipped with modules capable of managing large files, storing them in a cloud environment and extractin

241 experiment, there are links to downloadable files, such as RNA quantification matrices, clustering r

242 atic synchronization of files among isolated file systems.

243 ing and all their parameters) is stored in a file that can be used for reproducing the same analysis.

244 ot of all the commands, printed messages and files that have been generated during the recipe run.

245 ystallographic Information File (CIF) format files that maintains full compatibility to related data

246 Reason for filing the ERPO; characteristics of respondents; respond

247 positioned to help the most needy immigrants file their fee-waiver requests.

248 After importing quantitative data files, there are various data filtering and visualizing

249 For imaging files, this database-free approach was documented in the

250 alizable, making it possible for any variant file to be annotated with any isoform expression dataset

251 Our tool uses a simple configuration file to define the experimental arrangement and can be i

252 GLAD allows users to input multiple data files to create comparisons.

253 tomatically generates data and configuration files to create high quality and publishable circular pl

254 ary output, wig and bed files as well as csv files to export the location of all approximate k-mers f

255 We used Medicare inpatient files to identify index admissions for PCI and CABG from

256 he library is used to research the same data files to obtain the final result.

257 We have updated the structure of our data files to support complex DNA conformations, multiple DNA

258 to go from a set of raw data, such as fastq files, to publication-ready results and figures in one s

259 r submitting sequencing files via a separate file transfer mechanism.

260 esultant articles can be downloaded via both File Transfer Protocol for bulk access and a Web API for

261 all format (VCF) filtering software to yield file types readily analyzed by CLUMPAK.

262 KairosMS imports raw data from common file types, processes it, and exports a mass list for co

263 CRISPR-dCas9) to inform a Bt user constraint file (UCF) for Cello.

264 DSK, BCALM2 and Kraken were able to process files up to 16 GB, with linearly scaling CPU-times.

265 Tracks can be added via direct file upload or processed in real-time via links to files

266 odel generated from the gene transfer format file used during alignments reporting of the TPM values

267 Users can assemble ribo files using our RiboFlow pipeline that processes raw rib

268 ware tool that assesses the quality of FASTQ files using parallel programming.

269 The size reduction of an entire CRAM file varied from 2.2 to 7.4 fold, depending on the non-q

270 Here, we analyzed 10,383 variant call files (VCF) from the Cancer Genome Atlas (TCGA) and foun

271 iminating the need for submitting sequencing files via a separate file transfer mechanism.

272 ent Program (ACS-NSQIP) 2014 Participant Use File was queried to identify patients having undergone p

273 of Standard Transplant Analysis and Research files was undertaken on all deceased donors in the Unite

274 tained in a given Variants Call Format (VCF) file (we consider training and testing VCF files generat

275 When additionally linking an expression file, we show that GPress can reduce its size by more th

276 Quality Improvement Program participant use files were analyzed for patients who experienced anastom

277 was obtained using an intraoral scanner and files were compared in metrology software.

278 Requests for cine files were fulfilled by a department separate from diagn

279 in 2011-2017 ACS NSQIP Participant Use Data Files were included.

280 Pennsylvania birth and cancer registry files were linked by the state Department of Health, yie

281 For this purpose, the same raw data files were processed with the software packages MZmine2,

282 The patient's medical files were re-examined, including laboratory, radiology

283 vider Analysis and Review (MEDPAR) Inpatient Files were reviewed to identify Medicare patients who un

284 ere accessed over 133 days and 318 668 index files were stored in a local database.

285 Digital scanned files were used for quantification of FGG surface area (

286 ion Examination Survey with linked mortality files were utilized.

287 rface with many ways for users to edit their files which makes the task of logging user actions chall

288 ngle, bifacial stem cell in each radial cell file, which confirms the classical theory of a uniseriat

289 tated and transformed into protein data bank files, which are downloadable by researchers worldwide.

290 ert chemists and recorded in reusable recipe files, which are executed by a modular continuous-flow p

291 ce will benefit from providing analyses' log files, which contain typically reported parameters (e.g.

292 in the form of raw signal contained in fast5 files, which must be compressed to enable efficient stor

293 analytical parameters are recorded in excel files while a novel classification system is used which

294 zip (the current de facto compressor for GFF files) while being able to retrieve all annotations for

295 icare patients within the 5% enhanced sample file who were diagnosed with new incident CLI between 20

296 5 August 2019) are downloadable as a single file with accompanying metadata.

297 constructed pipelines can be exported as XML files with all of the parameter settings for reusability

298 roarray data is typically presented as excel files with limited visualization and interactivity.

299 g the Illumina Nextera XT protocol and FASTQ files with raw reads uploaded to the ARESdb cloud platfo

300 rticle incorrectly matched the supplementary files with their titles.