Search Results for "using"
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Showing 14 open source projects for "using"
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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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Retool your internal operationsBuild internal software that meets enterprise security standards without waiting on engineering resources. Retool connects to your databases, APIs, and data sources while maintaining the permissions and controls you need. Create custom dashboards, admin tools, and workflows from natural language prompts—all deployed in your cloud with security baked in. Stop duct-taping operations together, start building in Retool.
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Amplicon_Sequencing_Worfklow
Analyzing amplicon data from sequences to stats
...There are also instructions provided in case you are running these analyses via a computing cluster/Slurm workload manager. You can choose to go through the workflow using either an Rmd script, an html file, or a PDF, or via the homepage link provided. If you have questions or concerns, please don't hesitate to reach out. Thanks! -
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Seqs Extractor is a useful tool, and can reduce ambiguities in analyses which uses BLAST command ine, commonly in the next generation sequencing, Transcriptomics, Proteomics, etc and help extract BLASTed sequences and sequences that contains microsatellites. Seqs Extrator also turns the BLAST command line more friendly.
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Seqping
Gene Prediction Pipeline for Plant Genomes
Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data -
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Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
...It can also process other types of light imaging data in general. FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data. -
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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SPANDx
Comparative analysis of haploid next-generation genome sequence data
SPANDx is your one-stop tool for identifying SNP and indel variants in haploid genomes using NGS data. SPANDx performs alignment of raw NGS reads against your chosen reference genome or pan-genome, followed by accurate variant calling and annotation, and locus presence/absence determination. SPANDx produces SNP and indel matrices for downstream phylogenetic analyses. Annotated, genome-wide SNPs and indels can also be identified if specified, and are output in human readable format. ... -
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ProtPOS
Prediction of PROTtein Preferred Orientation on a Surface
ProtPOS is a self-contained, lightweight, and easy-to-use software package for predicting the preferred orientation of protein on a given surface upon initial adsorption. It searches quickly for the low energy protein poses in all translational and rotational degrees of freedom of the protein with respect to the surface using particle swarm optimization. Each successful run returns the lowest energy orientation of the protein on the surface in PDB format, which is readily used for MD simulations. ProtPOS is implemented in Python, making use of the PyMOL library for generating protein conformations and calling GROMACS externally to calculate protein-surface interaction energies. ... -
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cnvOffSeq
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments. -
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QUASI is a toolkit to rapidly assess the quality of shRNA-Seq based data and call differential abundance using common statistical inference methods (DESeq, edgeR, baySeq).
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OrthoRBH
Rapidly identify orthologous cDNA sequences in related species
OrthoRBH is a tool/pipeline designed to identify families of protein coding transcripts/genes in related species using a reciprocal blast method. It can search through databases of full-length cDNAs, ESTs or mRNA-seq data. Optional assembly of candidate sequences allows assembly of contigs. It is suited to handling a mixture of EST and mRNA-seq sequence data. It performs batch blast searches, so it is ideal for large multi-gene families. After collecting candidate sequences, it performs sequence alignment and deposits sequences into a fasta sequence file for downstream molecular evolutionary analysis. -
Grafana: The open and composable observability platformGrafana is the open source analytics & monitoring solution for every database.
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Bioinformatic tools for analyzing an orfeome using translated ORFs and compares each ORF to the provided Orfeome/Proteome. Our script uses NCBI BLAST run locally and MySQL as the main engines in a new and interisting way. It is designed specifically for Poxvirus genomes, and provides the VACV-COP nomenclature and Cowpox Ortholog groups per each ORF. The BLAST stats are generated when compared to the Proteome you provide.
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denovo_solid_pipeline
Pipeline for small genome assembly using SOLiD sequencing technology
denovo_solid_pipeline (DSP) is a semi automated pipeline for short genome assembly using SOLiD sequencing data. The main features of the pipeline are the optimization of the number of read-correction runs and computational resources via dynamic programming. DSP also has the advantage over the currently available pipeline (denovo2) of generating more contigs suitable for further assembly steps, increasing the chances of detecting sequencing errors and/or polymorphic sites. -
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SOAPsv
SOAPsv: is a program for detecting the structural variation
...In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers. -
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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The High Throughput Sequence Analysis Pipeline uses freely available bioinformatics tools from NCBI, Phylip, EMBOSS and clustalw to identify and group closely related DNA samples. It can be run on *Nix systems linearly or in parallel using the SGE.
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