Search Results for "rnaseq"
Sort By:
Showing 27 open source projects for "rnaseq"
View related business solutions-
Red Hat Enterprise Linux (RHEL) on Microsoft Azure provides a secure, reliable, and flexible foundation for your cloud infrastructure. Red Hat Enterprise Linux on Microsoft Azure is ideal for enterprises seeking to enhance their cloud environment with seamless integration, consistent performance, and comprehensive support.
-
Our computer monitoring software allows employees, field contractors, and freelancers to manually clock in when they begin working on an assignment. The application will take screenshots randomly or at set intervals, which allows employers to observe the work process. The application only tracks activity when the employee is clocked in. No spying, only transparency.
-
1
This is not really a "final" dataset. While the analysis has to come as a secondary priority to other responsibilities, this data set can serve at least 2 purposes: 1) Provide an experimental public lab notebook / log for an on-going experiment 2) After a few processed data sets have been added, provide an intermediate citation In the meantime, the best citation to use is probably the GitHub...
-
2
rna-test
script for variant calling of RNA-Seq
rna_test.sh is a shell script to run GATK best practice for variant-calling in RNAseq. It uses STAR2.5 for alignment, HaplotypeCaller to call variants, and Annovar to annotate. It also employs STAR-Fusion, Cufflinks and Stringtie FPKM, HTSeq_count and BAM-readcount. Notice: STAR_gene_read and HTSeq_count are added. exac03nontcga is added. STAR-Fusion is added. Stringtie is added. Disable BQSR (-skb) opteion is added. New avsnp(150) is updated. use -dcov in SplitNCigarReads added... -
3
miRDeep*
MiRDeep*
Please cite: An, J., Lai, J., Lehman, M.L. and Nelson, C.C. (2013) miRDeep*: an integrated application tool for miRNA identification from RNA sequencing data. Nucleic Acids Res, 41, 727-737. We will create index for you if you tell us your interested species (j.an@qut.edu.au). download command line version "MDS_command_line_Vxx.zip" clicking "Browse All Files" please find miRPlant in sourceforge for plant miRNA prediction. -
4
misc genomics tools
Various scripts used in sequencing, annotation and RNAseq analysis
This is a collection of various programs developed in the course of a genomics project, involving the Pseudomonas strain NCIMB10586 These include * identifying and correcting errors in an (eg) pacbio genome sequence using illumina reads * prokaryotic sequence/genome annotation * RNAseq analysis - normalisation and collation of multiple samples as a group * RNAseq visualisation All scripts are provided on a 'best efforts' basis, however due to various system changes I do not guarantee... -
Calmerry is beneficial for businesses of all sizes, particularly those in high-stress industries, organizations with remote teams, and HR departments seeking to improve employee well-being and productivity
-
5
... paired and unpaired study design. More information can be found at http://rnaseq-mats.sourceforge.net.
-
6
XPRESSpipe
An alignment and analysis pipeline for RNAseq data
-
7
RNASeqBrowser
RNASeqBrowser: A genome browser for strand specific RNAseq reads
Strand specific RNAseq data is now more common in RNAseq projects. The most widely used visualization tool is the UCSC genome browser that introduced the custom track concept that enabled researchers to simultaneously visualize gene expression at a particular locus from multiple experiments. This paper introduces a visualization tool (RNASeqBrowser) that incorporates and extends the functionality of the UCSC genome browser. For example, RNASeqBrowser simultaneously displays read coverage, SNPs... -
8
PTESFinder
Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline
PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions... -
9
altanalyze
Alternative splicing and functional prediction analysis tool
AltAnalyze is a freely available, open-source and cross-platform program that allows you to take RNASeq or relatively raw microarray data (CEL files or normalized), identify predicted alternative splicing or alternative promoter changes and view how these changes may affect protein sequence, domain composition, and microRNA targeting. AltAnalyze is compatible with any RNASeq data (exons and/or junctions), several Affymetrix splicing sensitive array types (Gene 1.0, Exon 1.0, junction) as well... -
BigQuery Studio provides a single, unified interface for all data practitioners of various coding skills to simplify analytics workflows from data ingestion and preparation to data exploration and visualization to ML model creation and use. It also allows you to use simple SQL to access Vertex AI foundational models directly inside BigQuery for text processing tasks, such as sentiment analysis, entity extraction, and many more without having to deal with specialized models.
-
10
fusion-test
Script for fusion detection in DNAseq and RNAseq
fusion_test.sh is a shell script to detect fusion in DNAseq or RNAseq. It uses chimerascan, SOAPfuse, MapSplice2, FusionMap, fusioncatcher, TopHat and EricScript. The output files of chimerascan are further annotated by Jinja and Pegasus Fusion. ***Updated*** Note: EricScript uses old version of Samtools. Download the modified program and Samtools-0.1.19 here. An error in the configuration for fusioncathcer is corrected. FusionMap has been deprecated. It is changed to Oshell. The old... -
11
MIRA - Sequence assembler and sequence mapping for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and error corrected data usable, uncorrected not yet.
-
12
Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial
RNA-seq analysis is becoming a standard method for global gene expression profiling. However, open and standard pipelines to perform RNA-seq analysis by non-experts remain challenging due to the large size of the raw data files and the hardware requirements for running the alignment step. Here we introduce a reproducible open source RNA-seq pipeline delivered as an IPython notebook and a Docker image. The pipeline uses state-of-the-art tools and can run on various platforms with minimal... -
13
BioMinerQT
A genomic analysis query tool
BioMinerQT is a web-based tool that internalizes ChIPseq, RNAseq, bisulfite, and variant analysis into a searchable database. The goal of the BioMinerQT is to allow researchers to mine all the data that has been uploaded without the help of a bioinformatician. -
14
Cloudomics-for-AWS
AWS resources for Bioinformatics Workflows & Apps
Library of scripts used for authenticating researchers who submit bioinformatics datasets to an S3 bucket for analytics using AWS resources (Development start : 2015 as part of Cloudomics, formally www.mycloudomics.com) -
15
sgescripts
Scripts for sun grid engine
Collection of useful scripts for the Sun Grid Engine, including mostly RNAseq processing data -
16
HeatmapGenerator is a graphical user interface software program written in C++, R, and OpenGL to create customized gene expression heatmaps from RNA-seq and microarray data in medical research. HeatmapGenerator can also be used to make heatmaps in a variety of other non-medical fields. HeatmapGenerator is peer-reviewed published software (http://www.scfbm.org/content/9/1/30). Please cite: [Khomtchouk et al.: "HeatmapGenerator: High performance RNAseq and microarray visualization software...
-
17
tag-based RNA-seq
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
Download the latest updates from https://github.com/z0on/tag-based_RNAseq Tag-based RNA-seq is a cost-efficient method of measuring expression of eukaryotic protein-coding genes on a whole-genome scale. It is described in Meyer, Aglyamova and Matz, Mol Ecol 2011 ( doi: 10.1111/j.1365-294X.2011.05205.x ). This project provides the scripts and walkthoughs for initial sequence data processing (from reads to gene counts), including: - concatenating raw sequence files according to... -
18
DESN
Differential activE sub-Network (DEN): R/Bioconductor based package
Living cells are complex, dynamic, self-regulatory, interactive systems, showing differential states across time and space. Complexity of cellular systems is highlighted with the multi-layered regulatory mechanisms involving the interactions between bio-molecules (such as DNA, RNA, mi-RNA and proteins). These interactions are analyzed in the form of static networks. Likewise, number of experimental techniques like microarray, RNASeq allows quantification of cellular dynamics and aid... -
19
PRADA
PRADA : Pipeline for RNA-Sequencing Data Analysis
Massively parallel sequencing of cDNA reverse transcribed from RNA (RNASeq) provides an accurate estimate of the quantity and composition of mRNAs. To characterize the transcriptome through the analysis of RNA-seq data, we developed PRADA. PRADA focuses on the processing and analysis of gene expression estimates, supervised and unsupervised gene fusion identification, and supervised intragenic deletion identification. PRADA currently supports 7 modules to process and identify abnormalities... -
20
DeepView
DeepView: RNAseq Viewer
DeepView: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks -
21
EJCCMTools
Generation of EJCCM files from SAM/BAM files
EJCCMTools is a Java software package for compression of SAM or BAM files, performing subsequent gene or transcript expression profiling and visualizing gene read coverage profiles. This novel compression scheme reduces file size by a factor of 214 compared to BAM files while keeping the full ability to analyze and visualize gene and isoform expression levels. As a result of the compression EJCCM files are generated. These files can be indexed and queried using Tabix. -
22
miRPredict
microRNA prediction from next generation sequencing data
The project has been renamed to miR-PREFeR(microRNA PREdiction From small RNAseq data). The project is now hosted on github at https://github.com/hangelwen/miR-PREFeR . -
23
-
24
FunSys, a software that can be used to analyse differential expression data from RNAseq and can integrate these analyses with data from proteomic studies.
-
25
EXshuffle
Post-transcriptional exon shuffling detection from RNAseq data
Post-transcriptional exon shuffling (PTES) are exon reordering in a transcript comparing to their genomic positions. EXshuffle is a program for PTES analysis from RNAseq data. EXshuffle uses pairing information intersect with exons coordinates to detect robust PTESs in a reasonable time and memory usage.