🧬 Quantify hERV and transgenes from Bulk-RNAseq
Human Endogenous Retroviruses (hERVs) are ancient viral sequences embedded in the human genome. Transgenes are common in transgenic mouse models. To quantify them from sequencing reads, we need-- a) modify fasta and gtf files to include the their sequencing and annotation; b) a feature quantification algorithm to handle multimapping commonly seen for hERV and transgenes. Here I discussed the algorithms for feature quantification, and successfully quantified hERV and transgenes by implementing an EM algorithm.
May 27, 2025
🧬 EM algorithm, EM with max a posterior, full Bayesian inferences (variational Bayesian) used in auto-coder
EM algorithm, EM with max a posterior, full Bayesian inferences (variational Bayesian) which might be used in auto-coder
Apr 12, 2025
🧬 Smooth tests of goodness of Fit used in Stijn Hawinkel ’s plos one paper
Smooth tests of goodness of Fit used in Stijn Hawinkel ’s plos one paper
Apr 10, 2025
🧬 how good is negative binomial, why AI works for biology
how good is negative binomial
Apr 9, 2025
🧬 Seurat to analysis large sample size of bulk RNAseq. Discuss Wixcox is better for clinical samples
Seurat to analysis large sample size of bulk RNAseq. Discuss Wixcox is better for clinical samples
Apr 8, 2025
🧬 Spatial genomics presentation
What we can get from Spatial genomics is most meaningful? how to present?
Apr 7, 2025
🧬 Deep Neural Network to integrate scRNAseq and spatial genomics
What we can get from Spatial genomics is most meaningful? how to present?
Apr 7, 2025
🧬 Bayesian abundance statistics in PRCC
One sample abundance statistics, bayesian vs frequentist
Apr 6, 2025
🧬 Train a high-performance Yolov8 (CNN) model for histological analysis: data augmentation and combating overfitting by Active Learning
Yolov8, a deep learning tool to
Apr 5, 2025
🧬 CCA reasoning and integration discussion
what is CCA really doing? here we dicepher it and present the mathmatical intuition to appreicate its applicability. Also, discuss the integration.
Apr 3, 2025