Biostar Tutorials

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r cancer classification tutorial Tutorial

updated 2 days ago by Ram 37k • written 8.9 years ago by Nicholas Spies ★ 1.2k

1 result • Page 1 of 1

Recent Votes

A: What is a gene transcript?

Answer: How to select rows which has NA in any column in the dataframe in R?

Comment: no output from GATK CombineGVCFs

Answer: How to convert a for loop to a Job-array in LSF cluster

C: How does samtools markdup works?

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Teacher to LDT ▴ 90

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Comment: How to select rows which has NA in any column in the dataframe in R? by Amr ▴ 90

Thanks genius

Answer: Adding metadata to Visium Seurat object by Judit • 0

Assuming the barcodes in the Seurat metadata and in your data frame are in the same order, run one of the following commands in order to ad…

Answer: How to select rows which has NA in any column in the dataframe in R? by LDT ▴ 90

you can use the ``` library(dplyr) data %>% filter_all(any_vars(is.na(.))) ```

Comment: Adding metadata to Visium Seurat object by Ram 37k

What commands have you tried?

Comment: random list of coordinates of different lengths by Chironex ▴ 30

Fantastic, thanks a lot!

Answer: How to convert a for loop to a Job-array in LSF cluster by Pierre Lindenbaum 149k

ok, second answer with a `Makefile` using option `-j` SHELL=/bin/bash BAMS=$(shell ls -1 /path/to/*.bam) define run …

Comment: How to convert a for loop to a Job-array in LSF cluster by LDT ▴ 90

That's a nice suggestion, Pierre. I appreciate. I am a bit behind in next flow but your post boosts me to go in that direction even faster

Answer: How to convert a for loop to a Job-array in LSF cluster by Pierre Lindenbaum 149k

use a workflow manager like nextflow. e.g (not tested) params.bams="NO_FILE" workflow { ch1= ST_COVERAGE(pa…

Comment: random list of coordinates of different lengths by mmmmcandrew ▴ 170

Yes, this is exactly what you can accomplish with bedtools shuffle. Take a look at the documentation [here][1]. The shuffle tool will take …

Comment: random list of coordinates of different lengths by Chironex ▴ 30

Hi, thanks for your reply. I don't want exactly shuffle my coordinates. I have about 1300 coordinates and I want to create a new set of coo…

Comment: Cannot convert the inetgarted seurat object to the cds for monocle 3 by Nitin Narwade ★ 1.2k

First of all, it's a warning and not an error. I guess your cell data object has been created. As suggested in the warning either run `cl…

Comment: filtering samples before normalization step by rheab1230 ▴ 110

I went through gtex portal qtl site but in that there is no filter for samples.

Comment: no output from GATK CombineGVCFs by liyong • 0

Thanks Pierre for the tips I will give it a try with screen later.

Comment: no output from GATK CombineGVCFs by Pierre Lindenbaum 149k

don't use nohup. `nohup` is bad, among other things it mixes stdout and stderr, you don't know how and why it exited . You'd better use `sc…

Comment: DEGseq - 3 conditions by pingu77 ▴ 10

thank you! But after I should take the intersection of the genes that are DE in resB_A and resC_A, right? thank you!

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