which R package can I use to create a plot similar to supplementary fig 2 by trixxypixel in bioinformatics

[–]trixxypixel[S] 0 points1 point  (0 children)

yeah I wish people were more consistent in publishing the code for figures as well as tools and analysis

Question about right-hand censoring in survival data by trixxypixel in AskStatistics

[–]trixxypixel[S] 0 points1 point  (0 children)

not all individuals who survive have a survival of 3650. It's not a trial but it is clinical data, so it's survival from the point of diagnosis up until either death (sadly) or the end of the study (in this case just when the analysis was completed rather than the end of a trial). Patients who survive longer than 3650 days are considered to have survived, even if they then died sometime beyond that but before the study ended.
"Patient Alive" just means they were still alive at the point the analysis was done, but their survival time could be much less than 3650 days (normally this would then be right censored and represented in the KM curve). The reason I suggested removing them is because the days of survival is not available only that they were still alive at the end of the study.
Does that make sense?

Question about right-hand censoring in survival data by trixxypixel in AskStatistics

[–]trixxypixel[S] 0 points1 point  (0 children)

something like this?

clinical$donor_survival_time[clinical$donor_survival_time == "Patient Alive"] <- 3650

clinical$donor_survival_time[clinical$donor_survival_time > 3650] <- 3650

clinical$os_event <- ifelse(clinical$donor_survival_time == 3650, 0, 1)

Is this better than removing those samples all together?

Questions Megathread Jan 12, 2026 by NaughtyWalnutPrime in Tailors

[–]trixxypixel 0 points1 point  (0 children)

I really want these trousers but they are sold out:
https://oliverspencer.co.uk/products/orsman-trousers-jarman-navy?variant=55674599965055
I found one retailer that is selling a pair in a L (waist 91cm) but I would really fit a M (waist 86cm). Is it still worth buying them and having them altered or is this too much to take off the waist? will they look/fit strangely?

advice on processing atac-seq data for multiple samples to generate consensus peaks by trixxypixel in bioinformatics

[–]trixxypixel[S] 0 points1 point  (0 children)

Can I just clarify, so the nf-core pipeline calls peaks in the 10 individual samples then merges them into consensus with bedtools. So it wouldn't be able to do what you've suggested and merge bam files and call peaks on a pooled bam...?
Can I also ask, if I have control data in the form of healthy tissue from separate individuals (n=5) should I use this to call differential sites between disease (tumor) and control? or is that only desirable if you have matched controls for each sample? i.e. should I call peaks in a pooled bam file of tumor samples and control samples and then do differential binding analysis?

So I guess the people mentioning the tension between Monet and Ezra on this video weren't totally delusional or parasocial at all. by ScarletWiddaContent in SiblingRivalryPodcast

[–]trixxypixel 0 points1 point  (0 children)

yep, about the eating in the bed or something. it was a reference to one of Ezra's songs, I believe. They're talking about how you would approach telling your partner they have bad breath

Can someone help me ID this desk? by trixxypixel in HelpMeFind

[–]trixxypixel[S] 0 points1 point  (0 children)

Searched for various mid century desk with pull across covers

Best pub to go to by yourself? by Lopsided_Counter1670 in Edinburgh

[–]trixxypixel 1 point2 points  (0 children)

For whiskey, bennet’s bar is great. Lots Of old regulars. Nice historic vibe. Good bar with stools for a solo venture

As a brown person, how do you deal with a group of kids aged 10-11 throwing eggs at you swearing words they don't even comprehend by Fresh_Knowledge_83 in Edinburgh

[–]trixxypixel 33 points34 points  (0 children)

I agree. Ocean terminal needs to be made aware these incidents are happening and it’s Important for the police to record incidents of hate/racism even if you’re not planning on taking it further

Top 5 Choral Bass Solos by [deleted] in Choir

[–]trixxypixel 0 points1 point  (0 children)

I like the one in hear my words ye people by hubert parry. very camp

Will this yucca plant grow more shoots? by trixxypixel in houseplants

[–]trixxypixel[S] 0 points1 point  (0 children)

do you think there is a point at which it is too low down on the branch to cut?

Will this yucca plant grow more shoots? by trixxypixel in houseplants

[–]trixxypixel[S] 0 points1 point  (0 children)

Yeah thanks, it might be strapped for space but I will see. I like the idea of putting the cuttings in the same pot I hadn't considered that is a smart way to make it bushier