Search Results for "osf/motif" - Page 3
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Showing 149 open source projects for "osf/motif"
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NgAgo-gDNA
A tool for designing NgAgo gDNA for genome editing
1. What is NgAgo-gDNA bioinformatic tool? Natronobacterium gregoryi Argonaute (NgAgo) is a DNA-guided endonuclease suitable for genome editing in human cells. NgAgo binds 5' phosphorylated single-stranded guide DNA (gDNA) of ∼24 nucleotides, efficiently creates site-specific DNA double-strand breaks when loaded with the gDNA. The NgAgo-gDNA system does not require a protospacer-adjacent motif (PAM), as does Cas9(Gao et al., 2016 Nat Biotechnol). Based on these features, NgAgo-gDNA... -
2
PROMOT
A tool for finding functional motifs from aligned protein sequences
... The above command sets fitness threshold to 70%, number of choices per motif element to 2, and ignores the functional grouping of the amino-acids, asking to input the data from aligned.fasta and redirecting the tool output to output.txt. You can open output.txt to view the results of the execution. -
3
CRISPR-Offinder
a CRISPR guide RNA design and off-target searching to
Summary: Design efficient and specific CRISPR small guide RNAs (sgRNAs) is one of the keys for a successful application of CRISPR technology. Importantly, more and more new RNA-guided endonucleases with different protospacer adjacent motif (PAM) have been discovered. Therefore, there is an urgent need to develop a versatile tool to design sgRNA to satisfy the requirement of different RNA-guided DNA endonucleases. To this end, a flexible sgRNA design program named “CRISPR-offinder” was developed... -
4
NSCR
Nascent Strand Capture and Release Protocol, bioinformatics part
This project is the bioinformatics part of the NSCR protocol paper, including mapping reads to reference sequence, wiggle file generation, motif searching, stiffness and bendability analysis. -
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5
OpenMotif-Mac
Making old wine run on new wineskins, or something.
... Motif License: http://www.opengroup.org/openmotif/license/ Copyright (C) 2015, The Open Group Ltd., Cameron Kaiser (maintainer) and others. All Rights Reserved. -
6
Wcl
widget-set-independend widget library
Wcl is a widget-set-independent widget library. This is an old library which has been reactivated because it is used in a project that uses Motif. It provides a table widget (any possibly more) -
7
mCarts
A hidden Markov model to predict clustered RNA motif sites
Many RBPs recognize very short and degenerate sequences, with targeting specificity achieved by mechanisms such as synergistic binding to multiple clustered sites and modulation of site accessibility through different RNA-secondary structures. mCarts integrates the number and spacing of individual motif sites, their accessibility and conservation, which substantially improves signal to noise ratio. This algorithm learns and quantifies rules of these features, taking advantage of a large number... -
8
xmsvm
X motif storage volume manager
Small X11 motif storage volume manager for Linux. Used udisk, libdbus. -
9
chipexo
model based analysis of ChIP-exo data
... with higher sensitivity, specificity and spatial resolution, as evidenced by multiple criteria, such as motif enrichment, sequence conservation, nucleosome positioning, and open chromatin states. -
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10
EZ-Arch Linux
An Arch Linux based distro
This is another arch Linux based distro with an installer to make it slighly easier and also it is preferred to be kept on a UNIX like philophsy where the GUI is equipped with the Motif Window Manager as well as awesome, icwem and twm. As from version 1 there is 32 and 64 Bit versions of this OS. It is good for minimalist type OSes who are not interested in very heavy GUIs. Future Videos will be uploaded to Dailymotion.com and the project URL is on. http://www.dailymotion.com... -
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Minimalistic cross-platform compiler for Component Pascal language, subset of BlackBox Component Builder 1.6 RC5 (forked subsystem Dev), capable to produce stand-alone software from command-line.
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12
MITSU
Stochastic EM for transcription factor binding site motif discovery
MITSU is an algorithm for discovery of transcription factor binding site (TFBS) motifs. It is based on the stochastic EM (sEM) algorithm, which overcomes some of the limitations of deterministic EM-based algorithms for motif discovery. Unlike previous sEM algorithms for motif discovery, MITSU is unconstrained with regard to the distribution of motif occurrences within the input dataset. MITSU also has the ability to automatically determine the most likely motif width by incorporating... -
13
Game Engine-X
THIS SOFTWARE IS IN PRE-PRE-PRE-PRE-ALPHA. So don't really download it
This software is a game engine. It uses SDL1.2, OpenGL (Mesa3D), and GTK+3 It doesn't yet have OpenGL, GTK+ nor a Sound System. Game Engine-X (GE-X). -
14
The Paradox Framework
Generic PHP Application Framework
A collection of libraries to quickly deploy a website with error handling, templating and user accounts. Application based, easily expanded into any type of website required. -
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IMPACT is an integrated multi-read peak calling tool for ChIP-Seq data. IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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... MIT. Il suit le motif de conception Modèle-Vue-Contrôleur et imite le fonctionnement de Ruby on Rails. Il est développé par Cake Software Foundation.
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Debian Unstable/testing alpha.
Pre-Alpha Console distro for high performance Linux computing.
Basic Debian INTEL/AMD HPC console/desktop multi purpose. Linux for software devs/QA and thin laboratory clusters. MIC hardware, NUMA and live network memory and full IPv6 are supported. Final alpha release features: ======== * Usb image * General debian repos * VM optimizations * Hugepages by default * CGROUPs optimized by default * ALSA * Latest Debugging / Baremetal kernels * Full Haswell and MIC support in test * Full optimized python support * Full... -
18
PANDA
Passing Attributes between Networks for Data Assimilation
PANDA (Passing Attributes between Networks for Data Assimilation), is a message-passing model to gene regulatory network reconstruction. PANDA integrates multiple sources of biological data, including protein-protein interaction, gene expression, and sequence motif information, in order to reconstruct genome-wide, condition-specific regulatory networks. PANDA is also available in other programming languages, including: MATLAB/Octave: (1) https://drive.google.com/a/channing.harvard.edu... -
19
BRACIL
ChIP-seq analysis tool
Binding Resolution Amplifier and Cooperative Interaction Locator (BRACIL) is a blind-deconvolution model that integrates ChIP-seq coverage with motif discovery. BRACIL predicts binding site locations with high-resolution and also cooperative interactions in ChIP-seq data. -
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... to the predictions based on the above analyses, common names, GO terms, and EC numbers. The genes are also translated and run through transcript level computes, including a COG analysis, motif finding, and peptide signal identification. The pipeline produces a functionally annotated genome, including RNAs and various genome characteristics, creating a stepping stone for further analysis.
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Geomview
an interactive 3D viewing program
Geomview is an interactive 3D viewing program for Unix. Geomview lets you view and manipulate three- and higher-dimensional objects, and can also be used as a display engine by other programs to animate objects. Geomview supports OpenGL and uses a Motif X interface. -
22
cmotif
A method for mining conditional phosphorylation motifs
Phosphorylation motifs represent position-specific amino acid patterns around the phosphorylation sites in the set of phosphopeptides. The discovery of phosphorylation motifs is a very valuable work in bioinformatics. Although several algorithms have been proposed to uncover phosphorylation motifs, the problem of efficiently discovering a set of significant motifs with sufficiently high coverage and non-redundancy still remains unsolved. In this paper, we propose an algorithm called C-Motif... -
23
jCryptoTrader
Java crypto-currency exchanges trading client
.../RSI/Stochastic signals, etc) * Port to Android (only gui required, because it's Java) # Known issues: * BTC-e returns extremely insufficient history data * Skins "System", "Motif" and "GTK" doesn't work properly -
24
AS-peak
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
... (EJC) RNA immunoprecipitation in tandem (RIPiT) experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses. -
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X11::GUITest, is a Perl package, used for controlling applications by means of user emulation. This can be used to interact (SendKeys, ClickMouseButton, FindWindowLike, etc.) with applications running under an X Windows environment. Including applications built (GTK+, Qt, Motif, etc.) upon X11 / Xlib. You may find that this mechanism is easier to use then that provided by xautomation or xdotool.