ライフサイエンスコーパス: file format

1 in future as a reference for this important file format.

2 at as well as a new standard EMBL-Align flat file format.

3 such as a unified taxonomy scheme and output file format.

4 browser tracks for entire genomes in the wig file format.

5 grating the efficient genomic data structure file format.

6 ents a standardized specification of the SWC file format.

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

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

9 a standardized single-molecule dataset (SMD) file format.

10 le BEAST and BEAUti use exactly the same XML file format.

11 stored using the recently developed SBGN-ML file format.

12 r other relational database schemas and flat file formats.

13 s and can be printed or exported in standard file formats.

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

15 efficiency, and it can support several input file formats.

16 ay use to convert between various proteomics file formats.

17 to read and write the many mass spectrometer file formats.

18 nostic and can import data from a variety of file formats.

19 ich also has more information on its use and file formats.

20 one or more secondary structures in various file formats.

21 s, and modularized for extensibility for new file formats.

22 programs typically encode the data in custom file formats.

23 nload these results in different, convenient file formats.

24 lecular structures and dynamics trajectories file formats.

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

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

27 n and supports genomics datasets in standard file formats.

28 features of source-specific data schemas or file formats.

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

30 ext within a figure, and creating acceptable file formats.

31 b browser as well as a variety of annotation file formats.

32 diting and visualisation options, and export file formats.

33 efinery can read and write a wide variety of file formats.

34 f genome scale data from a range of standard file formats.

35 other structural variants from new sequence file formats.

36 and can work with a wide range of sequencing file formats.

37 ist that all imaging platforms support these file formats.

38 data sets and to support a variety of input file formats.

39 as well as support for BAM and BigWig/BigBed file formats.

40 family of databases: access through multiple file formats, access through Application Program Interfa

41 The software is file format agnostic and processes multiple time-resolve

42 oviz 2 is flexible and uses open, documented file formats, allowing users to integrate new analyses w

43 We present the GCTx file format and a suite of open-source packages for the

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

45 top of the CoreArray Genomic Data Structure file format and libraries packaged in the gdsfmt package

46 The combination of a general file format and open source makes Java Treeview an attra

47 ool to compress large LD matrices in an HDF5 file format and query these compressed matrices.

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

49 wo distributions were collected in flat text file format and using specially developed software, the

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

51 ia an advanced, high-performance, extensible file format and Web API for remote data access.

52 Results are available in text or graphic file formats and additionally can be output to relationa

53 he adoption of reference proteomes, standard file formats and benchmarking.

54 ity, while also offering a plethora of input file formats and convenience options.

55 MolBioLib is designed to work with common file formats and data types used both in genomic analysi

56 ral domains) from a variety of commonly used file formats and displays them graphically.

57 New file formats and external database annotations are suppo

58 brary was developed that supports Affymetrix file formats and implements two popular summary algorith

59 By supporting interoperability with multiple file formats and leveraging existing Biopython features,

60 s for reading and writing different sequence file formats and multiple sequence alignments, dealing w

61 atistical routines, tools for parsing common file formats and packages for manipulating sequences and

62 to support standard annotation and sequence file formats and produces publication-quality SVG output

63 By promoting the adoption of standard file formats and providing a comprehensive visualisation

64 PrecisionProDB supports multiple popular file formats and reference databases, and can generate a

65 spite the availability of numerous dedicated file formats and software packages, it is a widely held

66 ser's guide with a tutorial, a discussion of file formats and user options and additional details on

67 evelopment of phylo-grammars (using a simple file format) and automated parameterization of those gra

68 filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning

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

70 of software architectures, input and output file formats, and computing environments.

71 Popular file formats are natively read and bespoke data can also

72 Here, we introduce the K-mer File Format as a general lossless framework for storing

73 gle-cell cooler format is part of the cooler file format as of API version 0.8.9.

74 and produce an annotated sequence in Genbank file format as output.

75 The pipeline accepts multiple file formats as input including multiplexed or demultipl

76 e ability to accept many standard microscopy file formats as inputs and the introduction of a Google

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

78 lows users to upload trace files in standard file formats, automates basecalling using phred and phra

79 We propose the GBZ file format based on data structures used in the Giraffe

80 ated using a single analysis program without file formats being transformed from the original.

81 ormat that can address some problems of flat file formats by defining data structure and syntax, ther

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

83 this data, they must first be converted to a file format compatible with their tool of choice e.g., P

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

85 read, write, and manipulate a wide array of file formats (e.g. FASTA, FASTQ, BED, BEDPE, SAM, BAM, a

86 itors, (3) an output in an easily searchable file format enabling users to quickly sort through and i

87 The standard MMTF and BCIF file formats extend this approach with custom encoding o

88 Finally, many output file formats facilitate the sharing of data with other p

89 add SBGN support to their tools, whereas the file format facilitates the exchange of maps between com

90 database are described using a standardized file format, facilitating data exchange.

91 FASTQ is a standard file format for DNA sequencing data, which stores both n

92 as a high compression alternative to the BAM file format for DNA sequencing data.

93 To produce an open and extensible file format for DNA trace data which produces compact fi

94 d support for a MIM-specific markup language file format for exchange with other MIM-compatible tools

95 ownloaded in numerous formats including .gmt file format for gene set enrichment analysis or as a R/B

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

97 Adoption of a common, standard data file format for sharing raw single-molecule data and ana

98 FASTQ has emerged as a common file format for sharing sequencing read data combining b

99 Moltemplate is a file format for storing coarse-grained molecular models

100 We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from

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

102 AM sequence alignment files; the most common file formats for aligned next generation sequencing data

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

104 nomic (FG) data with diverse assay types and file formats for integration into analysis workflows tha

105 standards, and is capable of parsing common file formats for phylogenetic trees, performing basic tr

106 tions via Hastings ratios, and uses standard file formats for trees, alignments and models.

107 LDmat can also rebuild the original file formats from the compressed files.

108 es over the past year include changes to the file format, further development of the EMBLCDS dataset

109 The Variant Call Format (VCF) is a text file format generated during the variant calling process

110 ADAM is able to index many commonly used file formats generated by laboratory assays and therefor

111 cid or protein sequences (FASTA) and generic file format (GFF) files of the clipped sequence reads an

112 ual studies, accommodates a variety of input file formats, handles related and unrelated individuals,

113 Among these many alternatives, the SWC file format has emerged as a popular community choice, c

114 The OpenMSI file format has shown to provide >2000-fold improvement

115 ments, represented by the multiple alignment file format, have become a standard approach in comparat

116 d interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of prot

117 The reference CRAM file format implementation is in Java.

118 quantms is based on standard file formats improving the reproducibility, submission a

119 ition, the introduction of a new, normalized file format in 2010 has made for easier handling of the

120 tion (SAM) is one of the most widely adopted file formats in bioinformatics and many researchers use

121 rom and writes to several sequence alignment file formats including both sequential and interleaved f

122 Census 2 supports multiple input file formats including MS1/MS2, DTASelect, mzXML and pep

123 Site server accepts input in common chemical file formats including SDF and SMILES and provides tools

124 CrossMap supports most of the commonly used file formats, including BAM, sequence alignment map, Wig

125 es with commonly used programs using various file formats, including BIOM, and provides operations su

126 s, COMKAT image tool supports multiple image file formats, including the Digital Imaging and Communic

127 It can read all the commonly used file formats, including the new, compact ZTR files.

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

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

130 rinsic challenge of splitting reads-oriented file formats into self-contained partitions to avoid cos

131 The sparse allele vectors file format is an efficient storage format for large-sca

132 The fast and compact Skyline file format is easily shared, even for experiments requi

133 f-defining text archive and retrieval (STAR) file format is illustrated via examples to establish a b

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

135 ishes a unified and extensible multiplatform file-format, lazy representation of larger-than-memory d

136 ks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable

137 Furthermore, legacy bioinformatics file formats like GenBank do not provide enough informat

138 ultiple data files in common vendor-agnostic file formats, locate chromatographic peaks based on a ta

139 As a key point, the file format MAGE-TAB for proteomics has been developed t

140 MSLs is hampered by the lack of standardized file formats, metadata fields, and supporting ontology.

141 sed Proteomics Standards Initiative standard file formats: mzML, mzIdentML, and mzTab.

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

143 ed the modules for working with the standard file formats Newick, NEXUS and phyloXML behind a consist

144 ive graphical input or input in the chemical file format of SMILES.

145 ften hampered by a large variety of existing file formats, often containing similar information, and

146 Dfam is also available for download in flat file format or in the form of MySQL table dumps.

147 provided without the need to convert between file formats or learn different command line interfaces.

148 /Macromolecular Crystallographic Information File format (PDBx/mmCIF) is still not widespread.

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

150 ty of platforms with a myriad of proprietary file formats (PFFs).

151 atible with fasta, fastq, and specialized AS file formats presented in this manuscript.

152 ibrary that automatically parses 21 standard file formats (primary sequence annotations, per- and int

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

154 FAST5 (an application of the HDF5 standard) file format produced by ONT and provides a wealth of for

155 spectrum file formats (.ucsf), XEASY proton file format (.prot), and NMR-STAR format (.star).

156 The universal qPCR data exchange file format RDML is today well accepted by the scientifi

157 cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotatio

158 The single-cell cooler file format (scool) provides an efficient, user-friendly

159 atch the changes to MetabolomicsWB's 'mwTab' file format specification and enhancing the package's fu

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

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

162 al alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment m

163 as OME-TIFF and HDF5 with a next-generation file format such as Zarr will satisfy the majority of us

164 while providing integration into established file formats, such as fasta or gff, ensures comparabilit

165 vendor-specific libraries and vendor-neutral file formats, such as mzXML and mzData it can be difficu

166 tatistics as bigWig files, which is a common file format supported by many genome browsers.

167 riant Call Format (VCF)/BCF, and genomic VCF file formats, supporting a wide range of applications.

168 The OpenMSI file format supports storage of raw MSI data, metadata,

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

170 atasets well, and supports extensions to the file format that allow the results of additional analysi

171 Apache Parquet is a data file format that allows for efficient data storage, retr

172 r of assemblies grows, there is a need for a file format that can store the highly repetitive data sp

173 atabase is traditionally available in a flat file format that has a number of known shortcomings.

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

175 nalysis of hybrid sequence data in the "hyb" file format to enable customizable evaluation and annota

176 mat, we show how it can be added as a native file format to genomic libraries, enabling direct analys

177 introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibi

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

179 forts led to the development of interrelated file formats to exchange and reuse models in systems bio

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

181 ARKY assignment table (.shifts) and spectrum file formats (.ucsf), XEASY proton file format (.prot),

182 e provided as downloadable tables or network file formats usable in Cytoscape.

183 However, a lack of standardization of the file formats used has proven problematic when running se

184 IRootLab can handle some of the most popular file formats used in VBS.

185 nd tools are provided to read and write many file formats used to represent bioinformatic data.

186 ns in proteins as well as parsers for common file formats using a biologically meaningful data model.

187 The BigWig and BigBed file formats were originally designed for the visualizat

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

189 rates output into MS1/MS2/MS3, MGF, or mzXML file formats, which fulfills the format requirements for

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

191 ata representations, such as the common HDF5 file format widely used for single-cell data, that do no

192 We anticipate that the file format will find wide usage and embed AFM in the re

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

194 onment that enables users to view a range of file formats with ease.

195 often stored in proprietary and/or dead-end file formats without experimental context.