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questions
0
votes
1
reply
204
views
When should I use R-MarkDown over R-Script ?
r
rscript
rmarkdown
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Amr
▴ 160
0
votes
1
reply
440
views
mitch analysis report priority by standard deviation
mitch
standard_deviation
updated 3 months ago by
mark.ziemann
★ 1.9k • written 17 months ago by
Amr
▴ 160
0
votes
1
reply
450
views
Can I perform ANOVA test on rlog data of RNA sequencing counts?
rlog
ANOVA
updated 12 months ago by
andres.firrincieli
3.6k • written 12 months ago by
Amr
▴ 160
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog
PCA
vsd
updated 12 months ago by
ATpoint
82k • written 12 months ago by
Amr
▴ 160
4
votes
6
replies
1.1k
views
t-test to check if the cancer samples are significantly different than the normal samples using R
t-test
independent
12 months ago by
Amr
▴ 160
4
votes
6
replies
1.7k
views
What does it mean in GSEA when HALLMARK_UV_RESPONSE_DN is upregulated ? how it's down and upregulated?
GSEA
HALLMARK
15 months ago by
Amr
▴ 160
1
vote
0
replies
327
views
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
HALLMARK_UV_RESPONSE_UP
GSEA
updated 15 months ago by
ATpoint
82k • written 15 months ago by
Amr
▴ 160
2
votes
1
reply
554
views
Why we check adjusted p-value not p-value to check whether we reject the null hypothesis or not in DESeq2?
p-value
DESeq2
updated 15 months ago by
ATpoint
82k • written 15 months ago by
Amr
▴ 160
0
votes
0
replies
414
views
KEGG Pathway pathway in cancer
cancer
KEGG
16 months ago by
Amr
▴ 160
1
vote
2
replies
722
views
Can I get the read length from the count data file in R? How?
read_length
sequencing
updated 16 months ago by
seidel
11k • written 16 months ago by
Amr
▴ 160
0
votes
7
replies
904
views
How to filter genes inside a normalized count data file based on p-adjust value?
normalization
p-value
DESeq2
updated 17 months ago by
Ram
43k • written 17 months ago by
Amr
▴ 160
0
votes
3
replies
743
views
What is the difference between Frame shift ins mutation and In frame ins mutation?
mutation
Frameshift
DNA
updated 17 months ago by
Ram
43k • written 17 months ago by
Amr
▴ 160
5
votes
7
replies
1.5k
views
6 follow
How to connect with MobaXterm?
login
mobaxterm
ssh
offtopic
updated 17 months ago by
Ram
43k • written 17 months ago by
Amr
▴ 160
9
votes
19
replies
4.6k
views
6 follow
Relative frequencies of the nucleotides in Fasta files
fasta
updated 15 months ago by
xiaoleiusc
▴ 140 • written 3.1 years ago by
Amr
▴ 160
0
votes
2
replies
1.0k
views
How to plot the relative abundance of the most abundant genera?
relative_abundance
taxa.mean.plot
mean_relative_abundance
ggplot2
taxonomic
R
18 months ago by
Amr
▴ 160
3
votes
5
replies
841
views
How to clean taxonomy file for microbiome analysis in R?
taxonomy
microbiome_analysis
18 months ago by
Amr
▴ 160
0
votes
3
replies
767
views
How to visualize taxonomic data based on mean relative abundance?
relative_abundance
taxa.mean.plot
mean_relative_abundance
ggplot2
taxonomic
updated 18 months ago by
Jeremy
▴ 910 • written 18 months ago by
Amr
▴ 160
0
votes
0
replies
340
views
How to plot the relative abundance of the most abundant genera ? to visualize the taxonomic composition?
relative_abundance
barchart
abundance
mean
taxonomic
18 months ago by
Amr
▴ 160
0
votes
2
replies
701
views
How to custom colors in plot_ordination?
PCoA
plot_ordination
beta_diversity
18 months ago by
Amr
▴ 160
0
votes
1
reply
1.0k
views
How to change colors in boxplot in R?
ggplot2
box-plot
updated 18 months ago by
Ram
43k • written 18 months ago by
Amr
▴ 160
2
votes
5
replies
2.7k
views
How to make alpha diversity boxplot?
alpha_diversity
taxa
ASV
box_plot
shannon
updated 7 months ago by
yeah
• 0 • written 18 months ago by
Amr
▴ 160
4
votes
7
replies
2.4k
views
Error input data must be numeric in R, how to solve it?
error_numeric
ASV_file
R
18 months ago by
Amr
▴ 160
0
votes
3
replies
1.3k
views
How to plot all enrichment plots from GSEA in one single plot in python or R?
R
python
ES
GSEA
updated 17 months ago by
Ram
43k • written 18 months ago by
Amr
▴ 160
4
votes
7
replies
2.8k
views
Why we use adjusted p-value not p-value in differential gene expression analysis ?
p-value
adjusted-p-value
DGE
DESeq2
18 months ago by
Amr
▴ 160
0
votes
2
replies
623
views
Is there a setting in GSEA software to filter counts less than 10 before go for GSEA analysis?
GSEA
updated 18 months ago by
M.O.L.S
▴ 100 • written 19 months ago by
Amr
▴ 160
2
votes
1
reply
526
views
How to change the design DESeqDataSet to calculate log2foldChange in different way?
design
DESeqDataSetFromMatrix
condition
DESeq2
18 months ago by
Amr
▴ 160
0
votes
3
replies
1.2k
views
What is the best way to visualize the enrichment plots together after obtaining them from GSEA report?
ES
enrichment_plot
GSEA
updated 18 months ago by
Basti
★ 2.0k • written 18 months ago by
Amr
▴ 160
1
vote
1
reply
555
views
How to add color to specific groups of a boxplot in Python?
boxplot
python
pandas
updated 19 months ago by
seidel
11k • written 19 months ago by
Amr
▴ 160
1
vote
1
reply
729
views
Error in linear regression for multiple data-frames with matplotlib
linear_regression
matplotlib
updated 19 months ago by
GenoMax
142k • written 19 months ago by
Amr
▴ 160
1
vote
2
replies
530
views
How to change values on X-axis in matplotlib ?
matplotlib
python
pandas
updated 19 months ago by
Ram
43k • written 19 months ago by
Amr
▴ 160
2
votes
6
replies
930
views
How to add illustrative bar in ggplot2?
ggplot2
R
19 months ago by
Amr
▴ 160
2
votes
10
replies
2.1k
views
R-studio freezes error
RStudio
offtopic
updated 19 months ago by
Ram
43k • written 19 months ago by
Amr
▴ 160
2
votes
1
reply
534
views
What are the differences between significance, effect and standard deviation upon producing mitch reports?
mitch
significance
effect
StandardDeviation
R
19 months ago by
Amr
▴ 160
2
votes
1
reply
442
views
mitch report inquiries
mitch
R
19 months ago by
Amr
▴ 160
1
vote
3
replies
879
views
How Wald test calculates p-values in DESeq2?
Wald
p-value
DESeq2
19 months ago by
Amr
▴ 160
5
votes
2
replies
596
views
How to calculate effect size between two gene sets?
distance
effectSize
euclidean
updated 19 months ago by
GenoMax
142k • written 19 months ago by
Amr
▴ 160
2
votes
3
replies
655
views
Error in mitch in R
mitch
symbols
gene
R
updated 19 months ago by
rpolicastro
13k • written 19 months ago by
Amr
▴ 160
6
votes
5
replies
1.8k
views
How to select rows which has NA in any column in the dataframe in R?
dataframe
NA
R
updated 19 months ago by
rpolicastro
13k • written 19 months ago by
Amr
▴ 160
0
votes
2
replies
486
views
Error in mitch reports in R
mitch
R
updated 3 months ago by
mark.ziemann
★ 1.9k • written 19 months ago by
Amr
▴ 160
16
votes
8
replies
1.7k
views
6 follow
How to convert Ensemble Gene IDs to gene symbols or Entrez Gene IDs?
Gene
Symbols
mitch
IDs
updated 19 months ago by
Istvan Albert
100k • written 19 months ago by
Amr
▴ 160
1
vote
8
replies
17k
views
How to update rlang in R?
rlang
R
19 months ago by
Amr
▴ 160
4
votes
4
replies
707
views
How to take data from dataframe to put it in another dataframe in R?
dataframe
R
19 months ago by
Amr
▴ 160
5
votes
9
replies
1.4k
views
Convert Gene Ensemble IDs to Gene Symbols on R
Ensemble
R
Gene-Symbols
biomart
updated 10 months ago by
Ram
43k • written 19 months ago by
Amr
▴ 160
0
votes
1
reply
477
views
Depending on which counts number, the genes are overexpressed either up or down regulated in GSEA ?
gene
GSEA
geneset
updated 19 months ago by
jv
★ 1.8k • written 19 months ago by
Amr
▴ 160
7
votes
2
replies
7.0k
views
How to use biomart on R to convert Ensembl Gene IDs to Symbols?
IDs
R
biomart
Ensembl
Symbols
updated 19 months ago by
Ben_Ensembl
★ 2.4k • written 19 months ago by
Amr
▴ 160
2
votes
2
replies
606
views
Why the number of genes decreased after dds (DESeqDataSetFromMatrix)?
R
DESeq2
updated 7 months ago by
Ram
43k • written 19 months ago by
Amr
▴ 160
0
votes
3
replies
680
views
Why it is recommended to run samples from all groups together while performing DESeq although the design variables are not used when estimating the s…
DESeq2
GSEA
R
DEG
updated 19 months ago by
Istvan Albert
100k • written 19 months ago by
Amr
▴ 160
2
votes
3
replies
710
views
How to shade columns for dataframe in ggplot that has 2 dataframes?
ggplot2
R
updated 19 months ago by
zx8754
11k • written 20 months ago by
Amr
▴ 160
0
votes
1
reply
382
views
How to change colors for 1 data frame on a ggplot for combined 2 dataframes on R?
R
dataframe
ggplot
updated 19 months ago by
jv
★ 1.8k • written 20 months ago by
Amr
▴ 160
3
votes
2
replies
560
views
Why we perform coldata dataframe in normalization with DESeq2 on R?
dataframe
coldata
DESeq2
normalization
R
GSEA
20 months ago by
Amr
▴ 160
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