Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 21

DESeq2 multiple treatments, multiple time points, multiple cell lines

Note: this question has also been asked on Bioconductor Support I know there are a lot of questions asking similar things here on this forum and I...

Asked on 06/08/2021 by tnocs

2 answer

How to get matching pattern along with ID in a single command in grep?

I have a file containing multiple fast sequneces. For a specific consensus pattern as input, I extracted all the matching patterns from target fasta sequences withgrep -o -E "CC[GT]AAA[GC][AC]TT[GC]"...

Asked on 06/07/2021 by 20 21

1 answer

is it ok to use gene sets from an organism to enrich genes from a different organism?

Lets say I performed a single cell RNA sequencing analysis on mice blood samples. Eventually I am able to cluster cells together and get a set of genes of interest...

Asked on 06/07/2021 by gabt

0 answer

Brackets in .Rmd code blocks

I am making some R markdown documents for my stats class. I've noticed I get an error in some functions when I have a code block with {r} ...

Asked on 06/05/2021 by Angus Campbell

1 answer

Reading nested Map data structures in WDL

I'm having trouble getting WDL's read_json to work as expected when trying to create a Map[String, Map[String, String]] data structure. If I explicitly declare the data structure it works, as...

Asked on 06/05/2021 by blawney_dfci

0 answer

Retain only part of a file name and fasta header in fasta directory

I have a MainDirectory/hundreds_of_subdirectories/thousands_of_fastas structure. For each fasta in the bottom level, I am trying to change the file name as well as the first line in the file to...

Asked on 06/03/2021 by Malia W

2 answer

Selecting rows by partial match

I have a data frame one column is sample name likeSampleTCGA-VR-A8EX-01A-11D-A36I-01TCGA-L7-A56G-01A-21D-A25X-01TCGA-VR-A8ER-01A-11D-A36I-01TCGA-JY-A6FB-01A-11D-A33D-01TCGA-2H-A9GO-01A-11D-A37B-01TCGA-Z6-AAPN-01A-11D-A402-01TCGA-L5-A4OP-01A-11D-A25X-01TCGA-L5-A8NV-01A-11D-A37B-01TCGA-R6-A8W5-01B-11D-A37B-01TCGA-S8-A6BW-01A-11D-A31T-01TCGA-R6-A6Y0-01B-11D-A33D-01TCGA-R6-A8WC-01A-11D-A37B-01TCGA-S8-A6BV-01A-21D-A31T-01TCGA-L5-A4OJ-01A-11D-A25X-01TCGA-LN-A7HV-01A-21D-A350-01I want to subset samples which have partial match with these nameTCGA-IC-A6RETCGA-IG-A4QSTCGA-JY-A6F8TCGA-JY-A6FBTCGA-L5-A43ETCGA-L5-A4OGTCGA-L5-A4OHTCGA-L5-A4OJI have useddata[grepl(c("TCGA-IC-A6RE", "TCGA-IG-A4QS", "TCGA-JY-A6F8", "TCGA-JY-A6FB",...

Asked on 06/03/2021

3 answer

Differential Gene Expression with Replicates for some of the samples

[this question has also been posted on Biostars; some additional clarification from there has been copied into this question] I've been asked to analyse a set of...

Asked on 06/03/2021 by Reza Rezaei

0 answer

How to import large .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently....

Asked on 06/03/2021

1 answer

CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing

I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The problem is that I'm working with paired-end sequencing data,...

Asked on 06/03/2021 by Swimming bird

1 answer

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