How to download hg19 reference genome?
1. Solution 1 wget -O- ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chr{{1..22},X,Y,MT}.fa.gz | gunzip > ucsc.hg19.fasta 2. Solution 2 https://github.com/creggian/ucsc-hg19-fasta
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Ridge, Lasso & Elastic Net Regression with R | Boston Housing Data Example
{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) Load the libraries # https://stackoverflow.com/questions/4090169/elegant-way-to-check-for-missing-packages-and-install-them list.of.packages <- c("caret", "glmnet", "mlbench","psych") new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])] if(length(new.packages)) install.packages(new.packages, dependencies = T) # Libraries Needed library(caret) library(glmnet) library(mlbench) library(psych) # Data data("BostonHousing") data <- BostonHousing Data Partition set.seed(222) ind <- sample(2, nrow(data), replace = T, prob = c(0.7, 0.3)) train <- data[ind==1,] test <- data[ind==2,] Custom Control Parameters custom <- trainControl(method = "repeatedcv", number = 10, repeats = 5, verboseIter = T) Linear Model set...
How Could I Reply To "sorry"?
It's okay. Don't worry about it. Don't sweat. Not a big deal. Don't be. Or, slightly more formally, 'not at all' . It also depends on whether or not it is ok. Situation 1: Someone ran you over and broke your leg. Maybe you forgive them and accept their apology, but it's still a major problem for you. In this case you could say "I appreciate your apology." Situation 2: A friend stepped on your toe. "Please don't worry about it in the slightest." "Don't give it another thought." "That's very kind of you, but an apology is not necessary." "No actually, I like having my toe stepped on. Please do it again." (OK, maybe not this.) never mind no problem it's okay no biggie (slang) ( correct please if there is any mistake )
Plasmid Pooled Libraries
An Introduction to Pooled Libraries Pooled libraries represent a powerful tool for forward genetic screening, or identifying previously unknown genes that contribute to a phenotype. At their simplest level, pooled libraries are single preparations of many different plasmids. Plasmids within a given library have the same backbone, but they express or target different genes. Some libraries cover the majority of the genome, while others are restricted to certain gene sets. In cDNA libraries, each plasmid contains a unique cDNA. In shRNA or gRNA libraries, each plasmid contains a unique gene targeting sequence, but there are multiple sequences targeting each gene in the overall library. Barcoding libraries contain plasmids with unique, semi-random sequences that can be used for applications like lineage tracing or parsing the effects of expressing multiple genes at once. A well-designed screen can help you begin to understand what genes ...
Courses to learn
MIT 7.013 Introductory Biology, Spring 2011 https://www.youtube.com/playlist?list=PLUl4u3cNGP60xwJdwhP6Ado1IbQjvLsPD
Q&A about MAGECK from MAGECK google group
When to use RRA or MLE in MAGECK? The short answers is, if you compare with 2 conditions, use RRA. If you want to compare multiple conditions, use MLE. RRA generally give you better estimation of p values, but MLE is really powerful in terms of multiple condition comparisons. Reference: https://groups.google.com/forum/#!msg/mageck/91Jm6vOPFi8/w9TeuJ2-sVYJ How does MAGECK work? MAGeCK-VISPR usually calculates beta scores with 0-day as baseline. In other words, if you have 0-day, drug treated, and control samples, you will get two beta scores in mageck-vispr, one with drug treated samples, the other with control samples. MAGeCKFlute further tells you the difference between (drug-treated beta scores) vs (control beta scores). You can model the difference directly in MAGeCK-VISPR as well, by setting up the corresponding design matrix. However that is not a common approach and sometimes it's hard to interpret. MAGeCKFlute further gives you a more s...
How do I respond to an email, which was sent to me by a very senior person with an apology for replying me late?
He has followed the right email etiquette, and you must thank him for being so humble to you. Write briefly, no need to be unnecessarily verbose. You may write back something like, "Thank you very much for taking your precious time to reply my email. Please do not apologize. I can well understand your busy schedule, and appreciate the effort you have taken for writing back." ...and then come to your actual purpose of sending the email to him. Reference: https://www.quora.com/How-do-I-respond-to-an-email-which-was-sent-to-me-by-a-very-senior-person-with-an-apology-for-replying-me-late