Search Results for "rna-seq"
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Showing 28 open source projects for "rna-seq"
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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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Subread
High-performance read alignment, quantification and mutation discovery
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program. Subread aligner can be used to align both gDNA-seq and RNA-seq reads. Subjunc aligner was specified designed for the detection of exon-exon junction. For the mapping of RNA-seq reads, Subread performs local alignments and Subjunc performs global alignments. Subread and Subjunc were published... -
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relax
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using... -
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ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts.
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Lexical Analyzer Generator Quex
Generator of lexical analyzers in C and C++. Unicode Supported.
The goal of this project is to provide a generator for lexical analyzers of maximum computational efficiency and maximum range of applications. This includes the support for Unicode (UTF8, UTF16, ...) and a large variety of other encodings directly and via nested converters such as ICU(tm) and IConv. Sophisticated buffer handling allows to operate on plain file streams, on sockets, or manually fed buffer content. 'Ready-to-build' examples explain related concepts and facilitate practical... -
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Contiki-BBS
Contiki BBS is a tiny, little and text based bulletin board system
Contiki BBS is a tiny, little and text based bulletin board system (BBS) server for the Commodore 64 homecomputer and a compatible ethernet cartridge (e.g. RRnet, 64NIC+). It will also run in a VICE emulator with ethernet support enabled. The BBS itself can be accessed through a standard telnet connection. Despite a floppy disk drive and the ethernet cartridge no further addon hardware is required (for emulation use VICE with ethernet support). -
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epidaurus
tumor epigenetic database
Epidaurus is a collection of epigenetic datasets including transcription factor ChIP-seq, histone ChIP-seq, DNase-seq, FAIRE-seq, DNA methylation, etc. It also includes commonly used genome features (GC content, conservation) and RNA-seq. A user friendly interface has been developed to interrogate and visuzlize these datasets. -
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The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.
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PWMScan
A Web-based genome-wide Position Weight Matrix (PWM) Scanner
PWMScan is used to scan a position weight matrix (PWM) against a genome or, in general, a large set of DNA sequences. The PWM is the most commonly used mathematical model to describe the DNA binding specificity of a transcription factor (TF). A PWM contains scores for each base at each position of the binding site. The TF binding score for a given k-mer sequence is then obtained by simply adding up the base-specific scores at respective positions of the binding site. PWMScan takes as... -
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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RNAfdl
RNA force directed layout
RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings. -
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MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.
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SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge... -
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olego
OLego – short or long RNA-seq read mapping to discover exon junction
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast... -
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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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A Scalable Multicore Code for RNA Secondary Structure Prediction
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ViNSS View
Vienna Notation Secondary Structure Viewer
ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing. -
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NeedlemanWunsch
Fast global sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ -
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SmithWaterman
Fast local sequence alignment for the masses!
MOVED TO GITHUB: https://github.com/noporpoise/seq-align An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ -
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The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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This is a set of programs to manipulate Commodore 64 Datasette tape files. These tools can convert a WAV file to a TAP file and vice versa, or extract PRG/SEQ files from a TAP file. Additional tools are planned to convert PRG/SEQ files to a TAP file.
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FRASS is developed for RNA Structure Comparison. It allows one to compare the 3D structures of two RNA molecules and to scan a database containing all the known RNA 3D structures against a single query.
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Code for predicting the 2-dimensional folding with minimum energy of a given RNA sequence. The code was written and originally released by Rune Lyngso.
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The program predicts the optimal folding of all consecutive substrings of length L of an RNA sequence of length N in O(NL) time. The algorithm is based on two papers: Wexler, Zilberstein, Ziv-Ukelson (2007), and Horesh, Wexler, Ziv-Ukelson ,Unger (2008)