Stepgram is a handy application that allows you to identify aberrations in the DNA data from array-Comparative Genomic Hybridization (aCGH) experiments. The program allows you to load the experiment data from a text file and apply an algorithm based on the Interval Score. You can set the algorithm parameters such as the threshold and the minimum difference. The results and exported to text files that can be used for generating graphs and diagrams.
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Similar to other tools like Genepi and Genomic Shifter, Pathway Studio™ ‘DiagramMaker’ is a tool that enables you to create a step-by-step workflow from one gene to another. This allows you to simulate the expression of a disease-related gene or protein by entering the name of the gene/protein and then the output you would like to see. The ‘DiagramMaker’ tool allows you to simulate the flow of data through specific pathways. For instance, you may enter that a specific gene is up-regulated in your tissue of interest. This may also include different proteins of interest that are involved in this specific disease. The software will analyze the expression of these genes and proteins. This may include the creation of a 3-D diagram showing the multiple location of expression of the gene/protein, e.g. in blood, brain, or other organ(s). DiagramMaker Genome-wide expression data allows you to analyze the expression of a gene that is expressed in multiple tissues. The software is easy to use. You just enter the name of the gene that you would like to analyze and then select the tissue that is of interest, the tissue where you see the gene as up-regulated, or the tissue where you would like to see the gene as down-regulated. The software will analyze the expression of the gene in multiple tissues and then create a step-by-step pathway to understand the data. The results are presented in a 2-D diagram and an interactive 3-D diagram. Click on any node in the diagram to see all the genes/proteins that are upstream of the selected gene. DiagramMaker Pathway-based expression data allows you to analyze the expression of a gene that is expressed in multiple pathways. The software is easy to use. You just enter the name of the gene that you would like to analyze and then select the pathway that is of interest. The software will analyze the expression of the gene in this pathway. The results are presented in a 2-D diagram and an interactive 3-D diagram. Click on any node in the diagram to see all the genes/proteins that are upstream of the selected gene. DiagramMaker Disease-based expression data allows you to analyze the expression of a gene that is expressed in multiple pathways. The software is easy to use. You just enter the name of the gene that you would like to analyze and then select the disease that is of interest. The
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• Analyzes the log profile to identify blocks of DNA that have a significant deviation from a distribution that arises from random noise. • Stepgram Free Download works on the principle of Interval Mapping and identifies an abnormal chromosomal region based on the interval scoring criteria. • Interval Mapping identifies the chromosomal region with a possible cytogenetic aberration, based on the analysis of the log profile of DNA copy number data in the experiment. • Stepgram mainly does two things, first it identifies the chromosomal region with a significant deletion or duplication. • Second it identifies regions that have copy number neutral. • Stepgram does this by determining whether the intervals are above a threshold or not. • Stepgram algorithm has been developed with user driven parameters like Threshold, Minimum Difference and frequency of loci with deleted or duplicated segments. • Once it identifies the chromosomal region, a list of loci are provided with their associated chromosomal positions, frequencies and average log2 values. • Export the results to a report file for further exploration and analysis. • Stepgram uses pair-wise Mann-Whitney-Wilcoxon U statistics to identify intervals with a significant number of probes above the threshold. • Stepgram provides user control of the algorithm parameters like Threshold, Minimum Difference and frequency of loci with deleted or duplicated segments. • Stepgram also provides user control of auto-threshold, which also helps in the selection of intervals for further analysis. Stepgram Filter Criteria • Does not contain Repeat elements • Does not contain any segment that has no value for any of the two probes in the region • Does not contain any segment that has more than 4 duplications, or more than 20 deletions • Does not contain any segment that has less than 2% of the probes being deleted • Does not contain any segment that has less than 0.4% of the probes being duplicated (Suggested minimum and maximum for Probe Statistics) Stepgram Use Cases • Tumor specific segment detection using array CGH. • Identify the copy number changes on chromosome for the identification of your disease. • Efficient identification of Copy Number Variation (CNV) in bacteria and yeast. • Identify chromosomal aberrations in cancer cells. • Identify the regions of the genome that are deleted or duplicated to detect single gene deletions or duplications. 2f7fe94e24
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Stepgram is a free, simple, free editing and analysis tool for aCGH genomic data. Stepgram can be used to quickly identify aberrant intervals, visualize genomic copy number changes, and export interval scores to spreadsheets. Stepgram can be used for any experiment, and does not require you to have the aCGH data in a tab-delimited text file. Main Features: Stepgram is a simple, easy to use, free program that allows you to quickly identify aberrant intervals from aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions. Use the included histogram analysis tool to identify a significant difference in copy number within an interval. Automatically detect repetitive regions and stop the analysis if the algorithm is unable to find a significant difference within a repetitive region. Generate graphs using aCGH data automatically, and export graphs to PDF files. Stepgram Tips & Tricks: Stepgram is a good, simple, free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data. Stepgram offers a feature to annotate intervals in aCGH regions and Stepgram is a powerful, and easy to use free editing and analysis tool for aCGH data.
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The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. Stepgram can be used to find de ned aberrations, is automatically applied to the data and will generate a results page. The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. Stepgram can be used to find de ned aberrations, is automatically applied to the data and will generate a results page. The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. The application is used to create easily to track aberrations in DNA data from array- Comparative Genomic Hybridization (aCGH) experiments. Stepgram can be used to find de ned aberrations, is automatically applied to the data and will generate a results page. Intuitive interface. Modularity. GUI. Commercial license. Method of operation. Applications for this module. Automated set up of aCGH experiments: Sequencing of tumour and normal tissue, from same sample, from different subjects. Sequencing of cancer cells from different patients. Sequencing of normal cells from different organs. Sequencing of different regions of the same sample. Support for chromosome level analysis. Compares the profiles of DNA samples against a database of normal profiles, in order to find differences between the two. The application automatically identifies areas where the DNA of the sample differs from the normal DNA. Contact us at support@genesketcher.com if you have any doubts or questions on the use of this module.Radical The most powerful thing that rings in the ears is the Radical’s loud, full sound. The biggest misconception about what makes an over the ear headphone truly great is that it has to sound great when you’re not wearing it. The Radical delivers a full tonal balance no matter if you are wearing it
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