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January | 2017 | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2017/01
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. Monthly Archives: January 2017. Confusion matrix terminology is taxicab trigonometry. January 3, 2017. Originally posted on Bits of DNA. What are confusion matrices? In the 1904 book Mathematical Contributions to the Theory of Evolution, Karl Pearson introduced the notion of contingency tables. Sometime around the 1950s the…. Read Article →. Follow us on Twitter! Follow this blog on Feedly! Sequencing QC...
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October | 2016 | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2016/10
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. Monthly Archives: October 2016. How to Use t-SNE Effectively. October 21, 2016. T-SNE stands for t-Distributed Stochastic Neighbor Embedding (t-SNE) and is a popular technique for dimensionality reduction. The technique was introduced by van der Maaten and Hinton in 2008. T-SNE is […]. Read Article →. Follow us on Twitter! Follow this blog on Feedly! Top Posts and Pages. Essential dplyr cheat sheet for R.
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FPKM, TPM, RSEM or RPKM!? QC metrics for RNA-seq quantification | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2016/04/27/fpkm-tpm-rsem-or-rpkm-qc-metrics-for-rna-seq-quantification
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. FPKM, TPM, RSEM or RPKM! QC metrics for RNA-seq quantification. April 27, 2016. There are many quantification methods proposed to quantify expression abundance of genes, transcripts, exons or splicing junctions. But we all want to use the best one, right? How cool is that? Here is the paper they have published:. Is available that permits users to submit other competing methods. To compare several competi...
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How to Use t-SNE Effectively | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2016/10/21/how-to-use-t-sne-effectively
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. How to Use t-SNE Effectively. October 21, 2016. Recently, t-SNE (a non-linear and non-parametric method) has been gaining some popularity in the genomics and proteomics field. T-SNE is often used to embed high-dimensional data into low dimensions for visualisation. (Fonville et al., 2013). Or read this blog. How to use t-SNE effectively:. How to Use t-SNE Effectively. Leave a Reply Cancel reply. You are ...
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How much sequencing coverage do I need? | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2015/05/25/how-much-sequencing-coverage-do-i-need
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. How much sequencing coverage do I need? May 25, 2015. How many times have you asked yourself this question? Possibly, far too many! I found a really nice coverage guide put together by Genohub. Much of the data was collected from published coverage saturation experiments, and you can also find all paper references for each guideline in the table. I think it really helps for quick assessments. When it com...
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thomasscarroll | Sequencing QC and data analysis blog
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Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. It seems we can’t find what you’re looking for. Perhaps searching can help. Follow us on Twitter! Follow this blog on Feedly! Top Posts and Pages. Should you transform RNA-seq data: Log, VST, voom? Essential dplyr cheat sheet for R. Make slides with IPython notebook. How to Use t-SNE Effectively. Calculate nucleotide frequency with Rsamtools pileup. Tools for quality control of RNA-seq and ChIP-seq data.
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Make slides with IPython notebook | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2015/02/22/make-slides-with-ipython-notebook
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. Make slides with IPython notebook. February 22, 2015. I like using IPython notebook. In my projects, it’s a great way of combining text, code and plots. A bit like using R Markdown with RStudio, you can convert your notebook files to PDFs or HTML files. You can also show math formulas, embed images, videos and webpages. To start a IPython notebook just type:. Ipython notebook Example Ipython.ipynb. Users...
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Sequencing QC and data analysis | Sequencing QC and data analysis blog
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Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. Author Archives: Sequencing QC and data analysis. Statistics for biologists – a Nature collection. March 13, 2015. By Sequencing QC and data analysis. Read Article →. Follow us on Twitter! Follow this blog on Feedly! Top Posts and Pages. Should you transform RNA-seq data: Log, VST, voom? Essential dplyr cheat sheet for R. Make slides with IPython notebook. How to Use t-SNE Effectively. A way to fix the n...
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Assessing ChIP-seq sample quality with ChIPQC | Sequencing QC and data analysis blog
https://seqqc.wordpress.com/2015/02/02/assessing-chip-seq-sample-quality-with-chipqc-4
Sequencing QC and data analysis blog. Sequencing Quality Control, statistics and bioinformatics blog. Assessing ChIP-seq sample quality with ChIPQC. February 2, 2015. Are you looking to get a quick assessment of the quality of your ChIP-seq data? The R package ChIPQC. Allows you to do just that. Here is an example of ChIPQC usage with ENCODE data. First, lets install ChIPQC from Bioconductor in R:. Source(http:/ bioconductor.org/biocLite.R) biocLite(ChIPQC). Samples = read.csv(samples.csv) samples. Our d...
