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Showing 64 open source projects for "text"
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AI-generated apps that pass security reviewRetool lets you generate dashboards, admin panels, and workflows directly on your data. Type something like “Build me a revenue dashboard on my Stripe data” and get a working app with security, permissions, and compliance built in from day one. Whether on our cloud or self-hosted, create the internal software your team needs without compromising enterprise standards or control.
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Outgrown Windows Task Scheduler?Windows Task Scheduler wasn't built for complex, cross-platform automation. Get a free diagnostic that shows exactly where things are failing and provides remediation recommendations. Interactive HTML report delivered in minutes.
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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Hydrogen Bond Analysis Tool (HBAT)
HBAT 2 is migrated from PERL to Python.
HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. HBAT 2 is migrated from PERL to Python. Latest Documentation: https://hbat.abhishek-tiwari.com/ Web Server Version: http://hbat-web.abhishek-tiwari.com Latest Github Release: http://github.com/abhishektiwari/hbat Citation: Tiwari, A., & Panigrahi, S. K. (2007). HBAT: A Complete Package for Analysing Strong and Weak Hydrogen Bonds in Macromolecular Crystal... -
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PlateEditor
PlateEditor, a free web application to work with multi-well plates
PlateEditor is a free web application to work with multi-well plates, from creation of layouts to data visualization and aggregation. It is primarily designed as a tool to help scientists working in the field of biology to simplify and fasten the process of data analysis. It is fully client-side: files are never transferred to the server, ensuring complete security and privacy of research data. It doesn't require any installation. - PlateEditor is available at this... -
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Comet MS/MS search engine
Comet open source tandem mass spectrometry (MS/MS) search engine.
...Comet currently exists as a simple Windows or Linux command line binary that only does MS/MS database search. Supported input formats are mzXML, mzML, ms2, and Thermo RAW files. Supported output formats are tab-delimited text, Percolator pin, SQT, and pepXML Documentation and project website: http://comet-ms.sourceforge.net -
Atera all-in-one platform IT management software with AI agentsAtera’s AI agents don’t just assist, they act. From detection to resolution, they handle incidents and requests instantly, taking your IT management from automated to autonomous.
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YeastpRofileSpearman
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The data of TSS and TTS counts used to compute the cross-correlation profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting Rs values for the various shifts of variable coordinates with respect to TSS or TTS. 1) V. Pelechano et al., Nature, 497 (2013) 127-13. -
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MSP Builder 2
Converts text files (such as csv, tsv, txt) to MSP files
Take a list from a search and how do you use that as a search. Answer: As an MSP file. But how do you make one? Answer: With this app. Convert your csv etc files to MSP. You define the relationship (the mapping) and take it from there. Includes a couple of examples. -
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MSP2MGF
Convert MSP files to MGF files - Only you know why
MSP2MGF processes MSP data files (NIST standard text files for searching) It: converts MSP data files into MGF files (mascot generic format)., produces a new file with the same name as your input file's, allows you to change the mapping of MGF fields into MGF fields, has a command line interface so you can pass files in programatically. You: either drag and drop MSP files onto the window, or pass filenames though a command line argument. -
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Peak List 2 MSP
Simple peak list to MSP file converter
Peak List 2 MSP takes your ascii mass/intensity pair list (or lists) and swaps them into MSP format (NIST standard text files for searching). It: takes lists from the clipboard (or drag and drop), sorts them by mass, normalises intensities, rejects below a cut off (that you define), adds MSP headers, puts the result back in the clipboard (or a file), has a command line interface so you can pass files in programmatically, has an api so you can call it in your own code (should you feel the urge). ... -
Financial reporting cloud-based software.The software is cloud based and automates complexities around consolidating and reporting for groups with multiple year ends, currencies and ERP systems with a slice and dice approach to reporting. While retaining the structure, control and validation needed in a financial reporting tool, we’ve managed to keep things flexible.
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DrawGlycan-SNFG
Renders glycans and glycopeptides with frag. info using SNFG format
...How to Cite: DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information Kai Cheng; Yusen Zhou; Sriram Neelamegham Glycobiology (2017) 27 (3): 200-205 Source code also available at: https://github.com/neel-lab/DrawGlycan-SNFGv2 Abstract & Full Text: https://doi.org/10.1093/glycob/cww115 -
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TIES
A smart search engine for medical documents
TIES (Text Information Extraction System) is a clinical text search engine that uses Natural Language Processing techniques to extract medical concepts from free text clinical reports. It provides secure de-identified access to this information and has in built collaboration tools and honest broker functionality. It is licensed for academic use under the BSD license. -
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@Note2
@Note2 - A workbench for Biomedical Text Mining
Biomedical Text Mining (BioTM) is providing valuable approaches to the automated curation of scientific literature. -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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YeastpRofile
Software to calculate profiles around TSS and TTS of yeast mRNAs
...The data of TSS and TTS counts used to compute the profiles were taken from the work of Pelechano et al. (1). The input file must be a BedGraph formatted file based on yeast genome sequence release R64. The output file is a text tab-delimited table reporting R values for the various shifts of variable coordinates with respect to TSS or TTS. R related to each strand is also reported to verify that a similar profile is obtained in the two direction of transcription. 1) V. Pelechano, W. Wei, L.M. Steinmetz, Extensive transcriptional heterogeneity revealed by isoform profiling, Nature, 497 (2013) 127-13. -
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HIGH-THROUGHPUT TABULAR DATA PROCESSOR (HTDP) is Java application that is intended to facilitate data exploration and reduction tasks in large text files resulting from high throughput technologies, e.g. massively parallel sequencing or microarrays. The software has been optimized for microarray and deep parallel sequencing data, however it can accept any character delimited tabular data sets. HTDP can also import, process and convert Variant Call Format (VCF) files ver. 4.0, 4.1 and 4.2 (http://samtools.github.io/hts-specs/VCFv4.2.pdf). ...
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DicomReader is a simple Java Dicom files decipher. It handles headers and images within as well; data (headers and pixel-value images) will be saved into ascii clear text files. A pgm version of the image files is also provided.
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GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. -
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Mass Difference Calculator
Mass Difference Calculator with a Graph for MassLynx data
A Mass Difference Calculator with a graph for MassLynx. Bring in a text file with reference masses and then paste in or browse in another file with a list of mass/intensity pairs. Then look at the best matching points and see what the difference between reference and data comes out as. This is a companion app to ResCalc3 -
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CorNetMap
A tool for Gene Expression Correlation Network
Capabilities of CorNetMap: 1. Read data as tab-delimited text file. Can be used for analysis of any data set beyond gene expression. 2. Capable of both two-dimensional and multidimensional data analysis. 3. Calculate Pearson correlation and cross-correlation for analysis data with phase difference. 4. Generate correlation Heat-map and draws network map. 5. Save correlation data as text file. -
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PDBManip
PDBManip is a free program for editing PDB (Protein Data Bank) Files
...What discriminate between PDBManip and those programs is that PDBManip uses AngelScript language which is very similar to C/C++ language, to write scripts to do our editing tasks. I know that the text-manipulation script languages such as Awk and Perl are available, and many users, uses these to do their works. However, in developing PDBManip, I have customized scripting language, by adding predefined PDB related variables and functions, in such a way that a user with a very basic knowledge of programming can easily write very eligible scripts, even for very complicated editing and manipulating tasks. ... -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. ... -
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Visualization of Protein-Ligand Graphs
Compute protein graphs. Moved to https://github.com/MolBIFFM/PTGLtools
NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/ -
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Sequencia
Protein Primary Sequnece Analysis
...This work includes all the Physiochemical Properties- related to Primary Sequence Analysis under a common platform. JAVA, BIOJAVA were used under Platform Independent architecture. The Tool includes Properties of being offline where result can be stored in Text Format, here we can paste more than one sequence and also upload FASTA file to compute Parameters. -
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bsclient
An interactive FTP-like command-line BaseSpace download client
bsclient is an interactive text-based client for browsing and downloading files from Illumina BaseSpace. It has a simple interface simliar to FTP and can be used to easily download files onto a remote server or in any situation when the web-based interface is not accessible or desirable. Please note that current development on this project has moved to GitHub: https://github.com/jvolkening/bsclient -
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BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
