Search Results for "transcript"
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Showing 70 open source projects for "transcript"
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View all cloud assets of AWS, Google Cloud, Azure, Kubernetes, Digital Ocean in one place. Automates security misconfigurations of assets with guidance to resolve them. Covers far beyond basic checklists. It automatically evaluates the security misconfigs of the assets & provides step-by-step guidance to resolve them
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Comet is a flexible backup platform, giving you total control over your backup environment and storage destinations.
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SimpMusic
A simple music app using YouTube Music for backend
A simple music app using YouTube Music for the backend. -
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome... -
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PyExfil
A Python Package for Data Exfiltration
PyExfil was born as a PoC and kind of a playground and grew to be something a bit more. In my eyes it’s still a messy PoC that needs a lot more work and testing to become stable. The purpose of PyExfil is to set as many exfiltrations, and now also communication, techniques that CAN be used by various threat actors/malware around to bypass various detection and mitigation tools and techniques. You can track changes at the official GitHub page. Putting it simply, it’s meant to be used as a... -
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Google Cloud’s AI-powered APIs help you translate documents, websites, apps, audio files, videos, and more at scale with best-in-class quality and enterprise-grade control and security.
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EvidentialGene
Evidence Directed Gene Construction for Eukaryotes
... and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes. -
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Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
... by Picard Tools for calculation of our filtering metrics: Fusion Transcript Score (FTS). Further filtering is realized by a custom blacklist, our Promiscuity Score (PS) and Robustness Score (RS). Identified fusion genes are reported with evidence levels based on our filtering. This pipeline has been developed and optimized in a study of 806 AML patient samples (https://doi.org/10.3324/haematol.2021.278436). -
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ediViewer
View, Edit and extract transactions from (PESC) standard Edi Files.
View, Edit and extract edi transactions from PESC standard approved Edi files. The EdiViewer has been tested to work with the following [PESC standards] (https://www.pesc.org/pesc-approved-standards-1.html) 1. TS 189 Application for Admission to Educational Institutions 2. TS 130 Educational Record (Transcript) -
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LARA is software for musical analysis using (new) scientific methods for analysis and visualization. LARA is part of the core research: “Interpretation and performance” of the HSLU – Musik (University of Applied Sciences Luzern – Music depart
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footswitch2basic
Audio Transcription software for Linux (Vlc) with a foot pedal
Footswitch 2 (Basic) is a media player for transcribers on Linux. This version is a stripped down version of Footswitch2, containing only the absolute essentials for transcription. Written in python and using the python bindings for VLC it allows a transcriber to control the audio or video with a footpedal, and includes a set of macros that integrate into LibreOffice. This allows the transcriber to control the media player from within Libreoffice as well, making it useful for those who do... -
AlertBot monitors your website's full functionality around the clock so you can focus your time on more important things.
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myPower
Power monitoring program
myPower is a simple monitoring and logging program for the Raspberry Pi. It collects live power usage data from the LeChacal RPICT8 current HAT and CT Sensors. myPower logs the data to daily files calculating each day's KiloWatt Hour Usage. **myPower Remote App is Still In Development** The collected data can be viewed in a user friendly format with a line graph and pie chart. Monthly, Yearly, and lifetime KiloWatt Hour Usage can also be viewed and graphed using the "myPower Remote"... -
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RSCH8360WK10
Transcript 1
Spirituality in simulation -
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PPIXpress
specific protein interaction networks from transcript expression
Although protein-protein interaction networks are an ubiquitous component of modern systems biology, comparatively few efforts have been made to tailor their topology to the actual cellular condition under study. Since a simple reduction of the networks to the subset of expressed genes only scratches the surface of higher organisms’ regulatory capabilities, we propose the advanced method PPIXpress that allows to exploit expression data at the transcript-level and is thus able to also reveal... -
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RNASeqBrowser
RNASeqBrowser: A genome browser for strand specific RNAseq reads
..., InDels and raw read tracks with other BED and wiggle tracks -- all being dynamically built from the BAM file. Paired reads are also connected in the browser to enable easier identification of novel exon/intron borders and chimaeric transcripts. Strand specific RNAseq data is also supported by RNASeqBrowser that displays reads above (positive strand transcript) or below (negative strand transcripts) a central line. j.an@qut.edu.au -
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PPLine
SNP calling, annotation and gene/transcripts expression quantification
PPLine is a Python-based suite aimed to process raw RNA-seq or Exome-seq data. PPLine provides: - read mapping (STAR/Tophat2/bowtie/bowtie2), including novel splice junsctions discovery - gene and transcript expression estimation (HTSeq-count/Cufflinks) - SNP calling with BQSR and indel realignment (samtools/GATK) - variant annotation (Annovar) - novel transcripts discovery (Cufflinks) - predicting proteotypic peptides and creating ref/alt proteins fasta-database - integration of the results -
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DualTranscriptDiscovery
Transcript-discovery approach for gene feature delimitation by RNA-seq
This project contains Python scripts usable for a dual transcript-discovery approach that improves the delimitation of gene features from RNA-seq data in the chicken model. Documentation: http://bio.biologists.org/content/biolopen/suppl/2018/01/17/bio.028498.DC1/BIO028498supp.pdf Citation: Orgeur M., Martens M., Börno S. T., Timmermann B., Duprez D. and Stricker S. (2018). A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model... -
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SlideShare Downloader
SlideShare download
This utility allow you to download any presentation from slideshare. Even if the author disabled it. -
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MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
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MPprimer
a program for reliable multiplex PCR primer design
... dimerization, and the inability to separate and purify DNA amplicons of similar electrophoretic mobility. Results: A new program named MPprimer was developed to help users design primer sets for multiplex PCR with high reliability. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. -
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ViralFusionSeq [VFS]
Accurately discover viral integration events and fusion transcripts
VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. VFS... -
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riboshape
Predicting ribosome footprint profile shapes from transcript sequences
Riboshape is a suite of algorithms to predict ribosome footprint profile shapes from transcript sequences. It applies kernel smoothing to codon sequences to build predictive features, and uses these features to builds a sparse regression model to predict the ribosome footprint profile shapes. Reference: Liu, T.-Y. and Song, Y.S. Prediction of ribosome footprint profile shapes from transcript sequences. Proceedings of ISMB 2016, Bioinformatics, Vol. 32 No. 12 (2016) i183-i191. -
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Blogspot To Docx
Blogger To Docx
Created your blog online, or on your phone? Use BlogspotToDocx.exe to reverse engineer your blog to your original transcript/text. With no images and hyperlinks! In docx format! It uses your blogger RSS feed to extract your text. Blogger to docx. Made according to Google’s Blogger Data API. It's written with Java, you got to have java on your system or just download the Java JRE. http://java.com/download Unzip it and put it on your desktop. RaY -
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The Alu knowledgebase integrates annotations of human Alus that could be queried easily to unveil new properties of these common genomic elements. For each Alu element, the closest gene and transcript are stored, as well their functional annotation according to GO, the state of the surrounding chromatin and the transcription factors binding sites inside the Alu. Izaskun Mallona, Mireia Jordà, and Miguel A. Peinado. "A knowledgebase of the human Alu repetitive elements." Journal of biomedical...
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EESST
Email Exchange of Secondary School Transcripts
... official, transcript recipients can independently verify that transcripts received directly from students have not been altered in transit.
