Search Results for "command line replacement" - Page 3
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Showing 137 open source projects for "command line replacement"
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DimerRemover
Remove adapter dimers from NGS data
This program can be used to count or remove adapter dimers in fastq files. Using a provided adapter sequence, it generates variations of this sequence and stores them in a hash table. The reads can then be directly matched against the hash. It is far more time efficient than doing alignment. -
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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MendelScan
Variant scoring and linkage mapping for family exome sequencing
MendelScan is a tool for prioritizing candidate variants in family-based studies of inherited disease. -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
...The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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DeNovoCheck
DeNovoCheck: Inheritance analysis for NGS trio data
DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants. -
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Seqshell
A JAVA GUI for performing the function of Tophat and Cuffdiff
Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email address when the job is done. (You will need to modify the source code to change the content to meet your special needs) Run-time information will be displayed in a JAVA output window. -
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cnvHiTSeq
cnvHiTSeq is a set of tools for detecting CNVs using sequencing data.
cnvHiTSeq is a set of Java-based command-line tools for detecting Copy Number Variants (CNVs) using next-generation sequencing data. cnvHiTSeq uses standard BAM files as input. -
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GEPETTO - Gene Prioritization in Java
GEPETTO (GEne Prioritization ExTended TOol)
GEPETTO (GEne PrioriTization ExTended TOol) is an original open-source framework, distributed under the LGPL license, for gene selection and prioritization on a desktop computer that ensures confidentiality of personal data. It takes advantage of the data integration capabilities in the SM2PH-Central Framework(KD4v,MSV3d,BIRD,..), combined with in-house developed gene prioritization methods. It currently incorporates six prioritization modules, based on gene sequence, protein-protein... -
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JGBParser
jgbparser, gbk parser, genbank parser, bioinformatics
We present an alternative library for development of bioinformatics Java applications. a Java implementation of JGBParser was built. It consists in a library, able to analyze text files in the GenBank Flatfile (GBF) format. -
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Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files
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Javamony
A Student's Approach to the Phylogenetic Problem
Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem. Javamony is invoked as follows: java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ... Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve... -
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Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
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Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.
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This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...
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OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.
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PileLine (Pileup pipeLine) is a toolkit for efficient handling of genomic position (GP) files, produced by next-generation sequencing experiments. It is designed to be memory efficient by performing on-disk operations over sorted GP files.
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Soaplab is a generator of Web Services providing a programmatic access to command-line (and other) applications on remote computers (an example of its usage is available at http://www.ebi.ac.uk/soaplab/)
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A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
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Contemplate is a bioinformatics tool for finding cis-regulatory modules (CRMs) in noncoding genomic regions using comparative sequence data.
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A phologenetic supertree construction/assembly tool using triplet similarity as the objective function.
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This is a multi-threaded Java program that tries to maximise CPU utilization by separating and distributing the computational part of the work from the file reading and writing part by using separate threads.
