Search Results for "effect"
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Showing 12 open source projects for "effect"
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1
AlphaGenome
Programmatic access to the AlphaGenome model
...The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
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UPS-indel
Universal Positioning System of indels
UPS-indel is a tool for "Universal Positioning System" of indels. It can be used to compare indels to see whether they are biologically equivalent or not. It can also be used to find out redundant indels. Moreover UPS-indel can be used to compare indels called by different tools. -
3
ISVASE
identification of sequence variant associated with splicing event
To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently by RNA splicing mechanism. It is to be noted that about one third or a half of all disease-causing mutations effect RNA splicing. However, there is little bioinformatics tools to directly identify sequence variants associated with splicing events (SVASE) based on RNA-seq data. We developed ISVASE, a simple and convenient tool for identifying SVASE directly using RNA-seq data. Comparing with the existing software PVAAS, our method has several advantages such as stringent rule-depended filters and statistical filters in each step, detection sequence variants for known splicing events, identification sequence variants in two parts of splicing (junction) separately, detection junction shift events if providing known splicing annotation, evaluating splicing signal, comparing with known DNA mutation and/or RNA editing data, and short running time. -
4
PingPongPro
Find ping-pong signatures like a pro
...Please refer to: https://github.com/suhrig/pingpongpro Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs, predominantly active in the germ line. There, they limit the detrimental effect of transposons on the genome. They do so by forming a complex with Piwi proteins. The complex binds and then cleaves mRNA molecules of active transposons. The resulting mRNA fragments induce the production of more piRNAs, thus reinforcing the anti-transposon response in a feed-forward loop called the "ping-pong cycle". A key question in ping-pong cycle research is identification of piRNAs which are amplified through the cycle. ... -
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5
NOFI ranking
The Non-Outlier Fragment Ion ranking for enhaced DIA quantification
...The outline is as follows: 1) The input contains the list of SWATH fragment ion XICs from the identified and quantified peptides by software tools such as Skyline and OpenSWATH. 2) The first step in NOFI is the computation of the 4 attributes (RTd, FWHMd, IRd and IRrep) used to represent each fragment ion as a vector. 3) Multivariate outlier detection techniques are used to rank all the fragment ions from each peptide. 4) Several figures are generated (a pdf file) to visualize the effect of the Top-N fragment ions over different indicators. 5) The user can choose the number of top fragment ions per peptide, thereby utilizing the optimal subset of high priority Top-N NOFIs for quantification while excluding the impaired fragment ions. -
6
provean
Predicting the functional effect of protein sequence variations
PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. The prediction is based on the change, caused by a variation, in the similarity of query sequence to closely related sequences collected through BLAST. -
7
FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
8
Hierachical_DNAcoder
An Hierachical Approach to Multi-Reference Genome compression
...To increase the exact aligning rate, we also realign the approximately mapped and unmapped reads by changing the reference sequence or shortening the read length. Meanwhile, we further the study using “lossy” quality values through k-means clustering scheme and find its minute effect on downstream applications. The proposed method has achieved compression ratios from 0.5 to 0.65, which corresponds to space savings of 35%-50%, on experimental datasets. -
9
CoVEC
Consensus Variant Effect Classification
The package provides SVM models to be used with SVMlight (http://svmlight.joachims.org/) for drawing a consensus out of individual 3rd-party predictions about the effect of mutations. The 3rd party tools are SIFT, Polyphen2, SNPs&GO and Mutation Assessor. The package also provides a series of Perl modules and scripts to assist in the preparation of data. The modules can be used to build custom tools and pipelines, whereas the scripts provide basic executable implementations based on the modules. ... -
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10
Pontos
Pontos calculates distance matrices from DNA sequence alignments.
...It can handle gaps and ambiguities in different ways. Gaps can be: - all used; - all ignored; - ignored only at the ends of the sequences, in a pairwise manner; - ignored only at the ends, but now globally (in effect trimming the whole alignment to the farthest sequences from the ends). Ambiguities (things like R, Y, N, W, etc. in a DNA sequence) can be treated like: - consider ambiguities as always different; - consider ambiguity as partially different (e.g. R would be 0.5 different from A or G); - ignore ambiguities in each pairwise comparison; - remove all columns, globally, that show any ambiguity. ... -
11
CancerVaccine
In silico vaccination experiment to determine best vaccination schedul
This project is a simplified representation of the main immune system cells and their interactions. The aim is to simulate the effect of the introduction of a cancer vaccine cell which would stimulate the immune response against the tumor-associated antigen, and consequently against cancer cells themselves. In vivo vaccination experiments take very long to complete, so it would be useful to simulate these experiments such that the best schedule of vaccination is determined that would result in control of the cancer cell population. -
12
Web-based user interface for MAQ (Mapping and Assembly with Qualities), an Illumina / Solexa Deep Sequencing Reads (fastq format) mapping software. MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.
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