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10 results • Page
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Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
4 days ago by
rohitsatyam102
▴ 780
36
votes
14
replies
32k
views
14 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 22 days ago by
psschlogl
▴ 50 • written 3.3 years ago by
lavinia.gordon
▴ 160
0
votes
0
replies
239
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
25 days ago by
rohitsatyam102
▴ 780
0
votes
4
replies
439
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
19 days ago by
Coremine Medical
▴ 20
90
votes
48
replies
31k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 27 days ago by
Ram
41k • written 10.1 years ago by
Irsan
★ 7.8k
48
votes
30
replies
9.3k
views
11 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 29 days ago by
ATpoint
78k • written 7.7 years ago by
Ram
41k
19
votes
13
replies
7.9k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 27 days ago by
jude
• 0 • written 17 months ago by
ATpoint
78k
1
vote
0
replies
590
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 22 days ago by
Ram
41k • written 8 months ago by
Milad
▴ 10
2
votes
0
replies
934
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 16 days ago by
Ali
• 0 • written 10 months ago by
firestar
★ 1.6k
5
votes
0
replies
4.2k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
22 days ago by
GenoMax
136k
10 results • Page
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Recent Votes
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
C: Heatmap : why scaling ?
Answer: How do I download a list of genes involved in cellular metabolism (in humans) ba
A: Incomplete reactome.org all pathway level to ENSEMBL ID annotation files
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Brian Bushnell
19k
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Info.shi
▴ 30
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el24
▴ 40
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Recent Replies
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R
by
ohtang7
▴ 30
Thank you!! I really appreciate your help.
Comment: Making multiple box plots with relative abundance in R
by
rpolicastro
12k
In `scale_fill_manual` you have e.g. `"stray"` but in your data it's `"Stray"`. Just make sure the cases match.
Comment: How to use conumee segment mean for gistic input
by
sativus
▴ 10
Did you manage to find an answer to this question, i have done so myself, but would like to confirm that this methodology is sound?
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