Search Results for "genes" - Page 3
Sort By:
Showing 268 open source projects for "genes"
View related business solutions-
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
-
Our intuitive email marketing software to help you save time and build lasting relationships with your subscribers.
-
1
Epi-Gene
EASY HANDLING OF MICROBIAL GENOMES
Epi Gene can cluster the whole genomes into 3 categories of core, accessory and unique genes. It can build two types of panmatrixes (i) Binary Panmatrix based on absence and presence of genes. (ii) Panmatrix based on the identity of the sequences. Binary pan-matrix will be used to build a UPMGA tree and heatmap to further describe an evolutionary relationship. While the pan-matrix based on sequence identity can be used for further quantitative analyses. This package can only works on WINDOWS... -
2
hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
hppRNA package is dedicated to the RNA-Seq analysis for a large number of samples simultaneously from the very beginning to the very end, which is formulated in Snakemake pipeline management system. It starts from fastq files and will produce gene/isoform expression matrix, differentially-expressed-genes, sample clusters as well as detection of SNP and fusion genes by combination of the state-of-the-art software. The first version handles protein-coding genes, lncRNAs and circRNAs and includes... -
3
GPRED-GC
a Gene PREDiction model accounting for 5'-3' GC gradient
A new hidden Markov model (HMM)-based ab initio gene prediction tool for finding genes with highly variable GC contents such as the genes with negative GC gradients in grass genomes. -
4
DACO-algorithm
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein... -
Rent Manager is award-winning property management software built for residential, commercial, and short-term-stay portfolios of any size. The program’s fully customizable features include a double-entry accounting system, maintenance management/scheduling, marketing integration, mobile applications, more than 450 insightful reports, and an API that integrates with the best PropTech providers on the market.
-
5
rattransc
RatTransc: a rat long noncoding RNA database
Welcome to RatTransc Introduction Long intergenic noncoding RNAs (lincRNAs) play a crucial role in many biological processes. The rat is an important model organism in biomedical research. Recent studies have detected rat lincRNA genes from several samples. However, identification of rat lincRNAs using large-scale RNA-seq datasets remains unreported. Herein, using more than 100 billion RNA-seq reads in combination with RefSeq and UniGene annotated RNAs, we identify 39,154 lincRNA... -
6
ParBiBit
Parallel tool to search biclusters on binary datasets
ParBiBit is a parallel tool to accelerate the search of biclusters on binary datasets, especially useful for gene expression data. This tool receives as input the expression values of n genes and m samples in a file with ARFF extension and returns a file with the biclustering information. -
7
MPICorMat
Parallel tool to construct correlation similarity matrices
MPICorMat is a parallel tool to construct correlation similarity matrices as part of the procedure to generate gene co-expression networks. This tool takes as input a matrix with the expression values (a float value) for different genes observed from several samples. It is a parallelization of the first module of the RMTGenNet tool (https://github.com/spficklin/RMTGeneNet). RMTGeneNet users can exchange this CCM module by MPICorMat, benefit from its fast computation to generate the similarity... -
8
Snapshot Demo
Snapshot models the genes and reactions within human cells
Snapshot is a poly-omics model of the human cell allowing you to edit genes and see how it affects cell functionality and what diseases might arise. The full Genome scale metabolic model consists of the following: 92 Genes 53 Reactions 109 Metabolites 3 Cellular Compartments 7 Diseases Which can be found here for only £2!: https://www.scarboroughbiotech.com/ Note demo version is a much smaller genome scale model. -
9
FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.
-
Drive your organization forward with the right solution at the right price. AI-powered continuous accounting and ERP to support your growth now and into the future.
-
10
bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files... -
11
FEATnotator is a light weight, fast and easy to use, open source software program that annotates different kinds of next generation analysis data based on known reference genome annotation information. For SNP data, it also predicts the effect of SNPs in the protein coding regions on the codons involved and marks SNPs potentially affecting start and stop codons and splice sites. It also identifies features of user’s interest, such as genes, or biomarkers in the vicinity of the features...
-
12
GAPE
proteogenomic analysis software
... of annotated genes, identification of previously unidentified genes, protein level identification of alternative spliced variants and SAAV, biological interpretation, and global PTM discovery. -
13
Panacea
PAN And Core-gEnome Analysis
A tool to calculate the Pan-Genome of a set of annotated genomes -
14
-
15
VacSol
An in slico pipeline to predict potential therapeutic targets
... to identify putative therapeutic targets against the infectious agents. In current study we have developed an in silico, multi-threaded, configurable and scalable pipeline employing subtractive-reverse vaccinology analysis technique and named it VacSol (https://sourceforge.net/projects/vacsol/). The principle objective of the VacSol development is to screen out genes/proteins from microbial genome/proteome that could be employed as potential therapeutic targets -
16
CoreAlyze
Use core genes to assess the coverage and fragmentation of a gene set
CoreAlyze analyzes the coverage and completeness of a curated set of widely-conserved, mostly single copy in one or more input test genomes. The characteristics of this subset provide insight into the coverage and fragmentation of the input gene set as a whole. CoreAlyze places its findings in context with other gene sets, adding to the robustness of the results. CoreAlyze also provides phylogenetic and biological information about input genomes. -
17
GNAT
GNAT recognizes gene names in text and maps them to NCBI Entrez Gene
GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/. -
18
Microarray Integrator (MAI)
Microarray Integrator for heterogeneous human/mouse Affymetrix arrays
The Microarray Integrator is freely available programs to integrate heterogeneous Affymetrix microarrays for human and mouse. The cell-type-specific genes or condition-specific genes can be screened in the integrated microarrays by MAI result. -
19
FUNN-MG is a tool for functional analysis and visual networks involving genes and metabolic functions previously annotated. ## PREREQUISITES FUNN-MG does not require installation, however depends on the following items: # A network connection. # JRE version >=6. # R version 3.4.1 ## EXECUTION AND PARAMETERS FUNN-MG requests as input file the results obtained from the kaas tool (Moriya et al., 2007). For more information about execution access the README file...
-
20
wgssat_nbfgr
WGSSAT: SSR Annotation Pipeline
WGSSAT provides a Graphical User Interface pipeline to mine and characterize SSR from Whole genome data. This pipeline integrates prediction of genes, ncRNA, repeats and SSR from whole genome assembly and mapping of these predicted SSR on to the genome (classified according to genes, ncRNA, repeats, exonic and intronic region) along with primer designing and mining of cross-species amplification markers. The mining of SSRs from whole genome provides valuable information on the abundance of SSRs... -
21
BPGA
A tool for ultra-fast pan-genome analysis of microbes.
BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc. -
22
IGSA
Individual Gene Sets Analysis
IGSA (Individual Gene Sets Analysis) is an application software based on Java and R that leverages a powerful analytical capacity. It can be used for gene sets enrichment and samples clustering. In gene sets enrichment, IGSA takes account of the heterogeneity of genes expression in samples and the homogeneity at the functional level, trying to pick out more particular and more significant gene sets. In sample clustering, IGSA clusters the samples based on the significant pathways rather than... -
23
-
24
SimilarityViewer
Identify co-occuring genes in cyanobacteria
The SimilarityViewer allows the identification of genes co-occurring in subsets of 77 cyanobacterial organisms. The software is available as a MATLAB script and as stand-alone applications for Mac, Linux, and Windows computers. To install this program download the zip file appropriate for your system, unzip it, and follow the instructions in the README file. SimilarityViewer and the included data are licensed under the Apache License Version 2.0. If you use the SimilarityViewer... -
25
SnowyOwl
RNA-Seq based gene prediction pipeline for fungal genomes
... predictor Augustus with varied input parameters, and selectivity by choosing the models with best homology to known proteins and best agreement to the RNA-Seq data. SnowyOwl has successfully predicted genes in 26 novel fungal genomes. The pipeline can be installed locally for high throughput and control over configuration. It can also be run on a remote server through a convenient web interface for occasional use.