Search Results for "size"
Sort By:
Showing 36 open source projects for "size"
View related business solutions-
Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
1
UniversalMer
A CLI k-mer counting tool for multiple sizes of k at once.
UniversalMer is a k-mer counting tool for multiple size of k at once. It is available for DNA, RNA, and protein sequences. The program counts and summarizes the exact frequency of all k-mers from 1-mer to a user-defined maximum length (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in seconds. This program is designed for bioinformatics researchers and scientists. -
2
genppi
GENPPI: standalone software for creating protein interaction networks
Our software GENPPI is efficient because, for example, it creates interaction networks from the central genome of 50 species/lineages of Corynebacterium, with an average size of 2200 genes, in less than 40 minutes, on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships between species and obtained in Average Nucleotide Identity (ANI) analyzes. Also, It allows the user to define how he intends to explore the PP and CN characteristics through various parameters that let on the creation of customized interaction networks. ... -
3
Fusion Detection Pipeline
Fusion gene detection pipeline bundled into a Singularity container.
...Therefore, we developed a detection and filtering workflow bundled into a Singularity container for a streamlined and easy-to-use application. Arriba and FusionCatcher are utilized for fusion calling. Our filtering pipeline uses read counts generated by FeatureCounts and insert size estimation 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). -
4
Corona Tracker
Coronavirus tracker app for iOS & macOS with maps & charts
Coronavirus tracker app for iOS & macOS with map & charts. https://coronatracker.samabox.com/ -
Stop Cyber Threats with VM-Series Next-Gen Firewall on AzureGain integrated visibility across all traffic in a single pass. Deploy Palo Alto Networks VM-Series to determine application identity and content while automating security policy updates via rich APIs.
-
5
MaxBin
An automatic tool for binning metagenomics sequences
...Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work. -
6
proTRAC
Use proTRAC to annotate genomic piRNA clusters
proTRAC detects genomic piRNA clusters. It considers all the relevant features of mapped sequence reads like the amount of 1U/10A, size and strand bias to ensure a high specificity. -
7
mfsizes
Multi-FASTA sequence (DNA or protein) statistics calculator.
A simple command-line utility to calculate biological sequence (DNA or protein) sizes in a (multi) FASTA file. It gives averages, GC (or methionine) content, N50, N90, N95, number of N's, and total bases, and can also report by codon if requested. -
8
datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
...Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. ... -
9
SUPERmerge
ChIP-seq coverage island analysis algorithm for broad histone marks
...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 is especially useful for investigating low sample size ChIP-seq experiments in which epigenetic histone modifications (e.g., H3K9me1, H3K27me3) result in inherently broad peaks with a diffuse range of signal enrichment spanning multiple consecutive genomic loci and annotated features. -
Stop vibe-debugging.AppSignal's MCP server hands Claude, Cursor, or Zed your real errors, traces, and the deploy that shipped them. AI writes the fix; you review the diff.
-
10
Fast Neurite Tracer
Semi-automatic neurite tracing with tera-bytes of imaging data.
...FNT is designed to be * accurate in tracing (each tracing step needs your confirmation), * fast (operations using computer mouse is reduced with automatic searching), * scalable (large volume data of tera-bytes in size are supported). Other features include * the results can be exported to SWC files, * automatic detection of cycles during tracing, * support for data of multiple channels, * support for both 8-bit and 16-bit image data. -
11
VCF Explorer
A desktop application for analyzing whole genome VCF files
he decreasing cost high-throughput technologies led to a number of sequencing projects consisting thousands of whole genomes. The paradigm shift from exome to whole genome brings a significant increase in the size of output files. Most of the existing tools which are developed to analyze exome files are not adequate for large VCF files produced by whole genome studies. In this work we present VCF-Explorer, a variant analysis software capable of handling large files. Efficient memory management of the program and the elimination of preliminary parsing step enable to carry out the analysis at ordinary computers. ... -
12
COPEread
Connecting Overlapped Pair-End Reads
COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research. The full citation: COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly Binghang Liu; Jianying Yuan; Siu-Ming Yiu; Zhenyu Li; Yinlong Xie; Yanxiang Chen; Yujian Shi; Hao Zhang; Yingrui Li; Tak-Wah Lam; Ruibang Luo Bioinformatics (2012) 28(22): 2870-2874; doi: 10.1093/bioinformatics/bts563 -
13
Transcriptome assembly ORA
Reference-based transcriptome reconstruction software
...It needs a SAM file with the reads aligned on the reference genome and (optional) a gff file with the position of genes on the reference genome. It provides in output the positions of the transcripts identified, the transcripts names based on the genes present on the gff file anf the size of UTR regions. -
14
CUDAlign
CUDAlign is a tool that aligns huge DNA sequences in CUDA capable GPUs
CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information: [1] Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. ... -
15
Virus QSP Modeling
C++ and Python code for simulating RNA virus replication
Stochastic simulation model of poliovirus Sabin-to-Mahoney genetic state transition (C++ code). Models genotypes, virus populations, and quasispecies cloud. Simulates replication error and copy-choice recombination. Various parameters guiding the model are user-specified. Python code post-processes simulation output to produce report files. -
16
FASTQSim
NGS data characterization and in silico read generation
FASTQSim is a tool that provides the dual functionality of Next-Gen Sequencing dataset characterization and metagenomic data generation. FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with matching error profiles. FASTQsim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. ... -
17
GUItars
GUItars is designed for the analysis of high throughput RNAi data.
...GUItars's user-friendly graphical interface enables rapid analysis of RNAi and small molecule screens. GUItars uses SSMD for hit selection, which is preferred for its ability to diminish sample size effects and the false hit rate, making it superior to other widely used HTS analysis methods. The program can handle the analysis for screens without replicates as well as with replicates. For comparison purposes, non-SSMD-based methods such as percent activity, z-score, and t-test are also provided as scoring options. Version 2.1 released: several bugs fixed. ... -
18
Bacterial Makeup Explorer
Bacterial Make eXplorer analyses bacterial genome ortholog maps
BMX (Bacterial Makeup eXplorer) computes the core genome size and composition from orthologous maps. -
19
Online Signature Verification
Real time signature verification using MATLAB and C#
Online Signature Verification technology requires primarily a digitizing tablet and a special pen connected to the USB port of a computer. An individual can sign on the digitizing tablet using the special pen regardless of his signature size and position. The signature is characterized as pen-strokes consisting x-y coordinates and pressure with the data being stored in a signature database. Dynamic time warping (DTW) and quadratic discriminant analysis (QDA) is used to get results where the system accepts 2% of forged signatures and rejects 5% of true signatures -
20
Coulson Plot Generator
Graphics generator for pie diagram matrix from spreadsheets
For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG. -
21
TopiaryExplorer has moved to GitHub. Find the new project info page here: https://github.com/qiime/Topiary-Explorer. If you need help or would like to add a bug/feature request, please do so there.
-
22
Prodar
Prodar searches the PDB for candidate protein structural alignments
...Prodar identifies partial matches, such that a relatively small section of the query structure may be matched against sections of other structures in the PDB regardless of the relative size of the chains. The intention is that the tool automatically identifies common domains and motifs in otherwise dissimilar protein structures. These can then be structurally aligned in a different tool to find an RMSD (Prodar just makes suggestions). Prodar encourages an interactive style of discovery, where searches are rapidly refined and rerun. ... -
23
Introminer
Extracts intronic information from annotated genomic sequence
Created by Julie Shay and Claudio Slamovits. Introminer reads a sequence file with genomic data that contains sequence and intron positions in genbank format. It extracts positional and sequence data as well as the intronic sequences and other important parameters to study gene architecture and intron evolution at a genome-wide scale. -
24
GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.
-
25
AgED
AgED - Analysis given Experimental Data
...This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in biology. Examples include the distinguishing of leaf shapes, fish sex, organ size and so forth. AgED is intended for scientific use only. Use and distribution of this technology is subject to the Java Research License included herein. AgED comes with absolutely no warranty.
