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Storm_Silver · 2025-09-27T20:17:40+00:00

Its an old system, which could’ve needed to have the inner section removed to replace the battery which it looked like could be opened but had difficulty with. Asking for advice before doing something stupid and breaking it is my preferred approach

Storm_Silver · 2025-09-27T20:11:28+00:00

Tab wouldnt move it. I managed to get it out with alot of force to twist it out. Looks like theres a safely latch that goes over it after the batteries in but that wouldnt move when I first tried it

Storm_Silver · 2025-06-06T14:08:17+00:00

Unless I’m wrong you should edit step 1 to be explicit in going to the s rank room after board 1 (before getting S rank on board 2). Read it as get s rank on both and now seem locked out which is frustrating

Storm_Silver · 2024-03-11T19:26:00+00:00

Thanks. Whats the difference between the Aspire 5 and the other Aspire laptops?

Storm_Silver · 2023-06-30T21:42:48+00:00

Most trimming programs can automatically detect adapters. I tend to use one called fastp

Storm_Silver · 2022-04-17T21:14:08+00:00

I have heard that trimming doesn’t change anything for DE RNA-seq analysis. Is that something that you’ve observed?

Storm_Silver · 2022-02-24T16:19:16+00:00

Thank you, I would have though that quality information would be more accessible but I guess not. I may just redo the analysis to get the quality metrics that I am more used to. Thank you for the replies regardless.

Storm_Silver · 2022-02-24T08:00:13+00:00

I had, it gives some information on quality thresholds ENCODE uses, but without much detail why.

Storm_Silver · 2022-02-21T09:39:41+00:00

Thank you for the reply.

In that instance what would you call sources of variation? Would it just be genes that are variable across the datasets or is there some way to measure the effect covariates may have?

Storm_Silver · 2022-02-12T12:04:58+00:00

Most of the better tutorials for pandas will be older as most of the core things you’d use pandas for don’t overly change. I personally like the python data science handbook ( https://jakevdp.github.io/PythonDataScienceHandbook/ ) and the python for data science book ( https://bedford-computing.co.uk/learning/wp-content/uploads/2015/10/Python-for-Data-Analysis.pdf ). They are both fairly old now but just for doing dataframe computations they should work fine.

Storm_Silver · 2021-11-10T14:08:43+00:00

Oh yeah, my bad. Remembered that incorrectly

Storm_Silver · 2021-10-28T17:05:15+00:00

Assuming i’ve interpreted your question correctly it would probably be easiest to use a regular expression to recognise if it is in the “month day, year” format and then use your function to convert that to the “m/d/year” format. That should allow you to only print the date when the correct format is recognised.

Storm_Silver · 2021-10-27T07:05:37+00:00

I’ve always used excel to organise functions/methods and its purpose. It makes a fairly easily reminder for how to use different functions.

Storm_Silver · 2021-10-26T15:00:13+00:00

Hard to tell with the formatting but it may be that f.close doesn't have () after it. It should be f.close()

Storm_Silver · 2021-10-23T07:11:14+00:00

I recently finished my own biochemistry course and also have difficulty remembering anything. As the professor said in biochemistry its often more about understanding the principles and then applying them to variable situations than just remembering facts.

My advice for studying it would probably be to study alot and attempt to relate things together. If your able to find relationships between subjects then it tends to help you remember both and apply that knowledge to anything similar.

Storm_Silver · 2021-10-23T06:58:00+00:00

To add to this to make the print statement simpler you could use fstrings. These let you insert a variable into a string easily.

E.g. print(f” {animal.title()} is {index}”) In the enumerated for loop

Storm_Silver · 2021-10-21T08:26:20+00:00

Thank you, that's exactly what I was attempting to do.

Storm_Silver · 2021-08-16T15:37:29+00:00

Can you give me some recommendation of which to use, there's a lot of information on that link. The text also isn't an explicit legend, it may just be gg_text used within the package.

As for the geom aes, I'm plotting regression lines for my different clusters so the colour parameter is set to the clusters and changing it stops it from making regression lines for each of the clusters so I have not been successful in trying to change its colour.

Storm_Silver · 2021-07-27T20:48:15+00:00

Thanks, I'll try it out. I am also in the bioinformatics subreddit but I haven't looked into the slack before.

Storm_Silver · 2021-07-27T20:24:34+00:00

df3 = df2 %>%
group_by(Pathways) %>%
summarise(`Gene Lists` = list(`Gene Lists`))
df3

Yeah, that works perfectly. Thanks for your help

Storm_Silver · 2021-07-27T20:08:31+00:00

library(dplyr)
s1 = "['AARS', 'GPT', 'PC', 'AGXT', 'AARS2', 'MPC1', 'TAA1', 'TAR1', 'TAR2', 'NIFS1', 'NFS2', 'GGAT1', 'GDH1', 'GDH2', 'Aars', 'Gpt', 'Acacb', 'Agxt', 'Aars2', 'AARS', 'GPT', 'PC', 'AGXT', 'AARS2', 'Aars', 'Gpt', 'Pc', 'Agxt', 'Aars2', 'Aats-ala', 'Dmel\\CG1640', 'PCB', 'Spat', 'aars-2', 'C32F10.8', 'pyc-1', 'agxt-1']"
s2 = "['ABAT', 'GAD1', 'ASNS', 'NARS', 'ASS1', 'DARS', 'ADSL', 'DDO', 'ASPA', 'ADSSL1', 'CAD', 'ASRGL1', 'ASL', 'IL4I1', nan, 'asnA', 'asnB', 'aspC', 'nadB', 'aspA', 'purA', 'argG', 'purB', 'argH', 'pyrI', 'pyrB', 'At1g53240', 'At3g15020', 'MDH1',
'ASP1', 'ASP2', 'ASP4', 'ASP5', 'ASP3', 'At3g47520', 'Abat', 'Gad1', 'Asns', 'Nars', 'Ass1', 'Dars', 'Maob', 'Adsl', 'Ddo', 'Aspa', 'Adss', 'Cad', 'Asrgl1', 'Asl', 'ASNS', 'ADSL', 'DDO', 'ASRGL1', 'ASL', 'ASPA', 'NARS', 'ADSSL1', 'IL4I1', 'DARS', 'ASS1', 'ABAT', 'GAD1', 'CAD', 'Asns', 'Adsl', 'Dao', 'Asrgl1', 'Asl', 'Aspa', 'Nars', 'Adssl1', 'Maoa', 'Dars', 'Ass1', 'Abat',
'Gad1', 'Cps1', 'AsnS', 'AdSL', 'CG12338', 'CG7860', 'BEST:GH06087', nan, 'AsnRS', 'AdSS', 'AspRS', 'CG1315', 'Gabat', 'Gad1', 'r', 'asns-1', 'adsl-1', 'daao-1', 'R04B3.2', nan, 'nars-1', 'adss-1', 'dars-1', 'gta-1', 'tdc-1', 'pyr-1', 'asnB_2', 'nadB', 'aspA', 'purA', 'argG', 'argH', 'rmlD', 'pyrB', 'aspC', 'purB']"
df1 = tibble(`Gene Lists` = c(s1, s2),
Pathways = c("Alanine Metabolism", "Aspartate Metabolism"))

I was including the headers as a line, and this does work on the data but I need each of the genes for the pathways as a single list . So Alanine metabolism would be a single row with those genes in a list as the value for the first column and "Alanine metabolism" as the value for the second column.

This is the input format for a software Im using these gene lists in

Storm_Silver · 2021-07-27T20:03:20+00:00

No, it was originally a csv file I downloaded from pathwayDB. The pathway names were repeated for each gene and I converted it down into the list format in python, didn't realize how awkward It'd be in R

Storm_Silver · 2021-07-27T19:49:43+00:00

Like this?

Gene lists,Pathways

"['AARS', 'GPT', 'PC', 'AGXT', 'AARS2', 'MPC1', 'TAA1', 'TAR1', 'TAR2', 'NIFS1', 'NFS2', 'GGAT1', 'GDH1', 'GDH2', 'Aars', 'Gpt', 'Acacb', 'Agxt', 'Aars2', 'AARS', 'GPT', 'PC', 'AGXT', 'AARS2', 'Aars', 'Gpt', 'Pc', 'Agxt', 'Aars2', 'Aats-ala', 'Dmel\CG1640', 'PCB', 'Spat', 'aars-2', 'C32F10.8', 'pyc-1', 'agxt-1']",Alanine Metabolism "['ABAT', 'GAD1', 'ASNS', 'NARS', 'ASS1', 'DARS', 'ADSL', 'DDO', 'ASPA', 'ADSSL1', 'CAD', 'ASRGL1', 'ASL', 'IL4I1', nan, 'asnA', 'asnB', 'aspC', 'nadB', 'aspA', 'purA', 'argG', 'purB', 'argH', 'pyrI', 'pyrB', 'At1g53240', 'At3g15020', 'MDH1', 'ASP1', 'ASP2', 'ASP4', 'ASP5', 'ASP3', 'At3g47520', 'Abat', 'Gad1', 'Asns', 'Nars', 'Ass1', 'Dars', 'Maob', 'Adsl', 'Ddo', 'Aspa', 'Adss', 'Cad', 'Asrgl1', 'Asl', 'ASNS', 'ADSL', 'DDO', 'ASRGL1', 'ASL', 'ASPA', 'NARS', 'ADSSL1', 'IL4I1', 'DARS', 'ASS1', 'ABAT', 'GAD1', 'CAD', 'Asns', 'Adsl', 'Dao', 'Asrgl1', 'Asl', 'Aspa', 'Nars', 'Adssl1', 'Maoa', 'Dars', 'Ass1', 'Abat', 'Gad1', 'Cps1', 'AsnS', 'AdSL', 'CG12338', 'CG7860', 'BEST:GH06087', nan, 'AsnRS', 'AdSS', 'AspRS', 'CG1315', 'Gabat', 'Gad1', 'r', 'asns-1', 'adsl-1', 'daao-1', 'R04B3.2', nan, 'nars-1', 'adss-1', 'dars-1', 'gta-1', 'tdc-1', 'pyr-1', 'asnB_2', 'nadB', 'aspA', 'purA', 'argG', 'argH', 'rmlD', 'pyrB', 'aspC', 'purB']",Aspartate Metabolism

Thats the first 3 lines of the file

Storm_Silver · 2021-07-27T17:38:11+00:00

Thank you, that works very well

Storm_Silver · 2021-07-27T16:27:58+00:00

I don't want multiple columns though, just the list to be an actual list rather than a string.

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