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0
votes
1
reply
376
views
When should I use R-MarkDown over R-Script ?
r rscript rmarkdown
updated 8 months ago by 86k • written 8 months ago by ▴ 180
0
votes
1
reply
564
views
mitch analysis report priority by standard deviation
mitch standard_deviation
updated 12 months ago by ★ 1.9k • written 2.1 years ago by ▴ 180
0
votes
1
reply
564
views
Can I perform ANOVA test on rlog data of RNA sequencing counts?
rlog ANOVA
updated 20 months ago by 3.8k • written 20 months ago by ▴ 180
4
votes
3
replies
1.3k
views
What is the difference between vst and rlog to perform PCA ?
rlog PCA vsd
updated 20 months ago by 86k • written 20 months ago by ▴ 180
4
votes
6
replies
1.4k
views
t-test to check if the cancer samples are significantly different than the normal samples using R
t-test independent
20 months ago by Amr ▴ 180
6
votes
6
replies
2.5k
views
What does it mean in GSEA when HALLMARK_UV_RESPONSE_DN is upregulated ? how it's down and upregulated?
GSEA HALLMARK
24 months ago by Amr ▴ 180
1
vote
0
replies
416
views
How can two contradicted gene sets be enriched in a cancer sample in GSEA analysis?
HALLMARK_UV_RESPONSE_UP GSEA
updated 24 months ago by 86k • written 24 months ago by ▴ 180
2
votes
1
reply
666
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 24 months ago by 86k • written 24 months ago by ▴ 180
0
votes
0
replies
511
views
KEGG Pathway pathway in cancer
cancer KEGG
2.0 years ago by Amr ▴ 180
1
vote
2
replies
843
views
Can I get the read length from the count data file in R? How?
read_length sequencing
updated 2.1 years ago by 11k • written 2.1 years ago by ▴ 180
0
votes
7
replies
1.2k
views
How to filter genes inside a normalized count data file based on p-adjust value?
normalization p-value DESeq2
updated 2.1 years ago by 44k • written 2.1 years ago by ▴ 180
0
votes
3
replies
1.4k
views
What is the difference between Frame shift ins mutation and In frame ins mutation?
mutation Frameshift DNA
updated 2.1 years ago by 44k • written 2.1 years ago by ▴ 180
5
votes
7
replies
2.1k
views
6 follow
How to connect with MobaXterm?
login mobaxterm ssh offtopic
updated 2.1 years ago by 44k • written 2.1 years ago by ▴ 180
9
votes
19
replies
5.4k
views
6 follow
Relative frequencies of the nucleotides in Fasta files
fasta
updated 23 months ago by ▴ 140 • written 3.8 years ago by ▴ 180
0
votes
2
replies
1.2k
views
How to plot the relative abundance of the most abundant genera?
relative_abundance taxa.mean.plot mean_relative_abundance ggplot2 taxonomic R
2.2 years ago by Amr ▴ 180
3
votes
5
replies
1.1k
views
How to clean taxonomy file for microbiome analysis in R?
taxonomy microbiome_analysis
2.2 years ago by Amr ▴ 180
0
votes
3
replies
945
views
How to visualize taxonomic data based on mean relative abundance?
relative_abundance taxa.mean.plot mean_relative_abundance ggplot2 taxonomic
updated 2.2 years ago by ▴ 930 • written 2.2 years ago by ▴ 180
0
votes
0
replies
449
views
How to plot the relative abundance of the most abundant genera ? to visualize the taxonomic composition?
relative_abundance barchart abundance mean taxonomic
2.2 years ago by Amr ▴ 180
0
votes
2
replies
875
views
How to custom colors in plot_ordination?
PCoA plot_ordination beta_diversity
2.2 years ago by Amr ▴ 180
0
votes
1
reply
1.2k
views
How to change colors in boxplot in R?
ggplot2 box-plot
updated 2.2 years ago by 44k • written 2.2 years ago by ▴ 180
2
votes
5
replies
3.4k
views
How to make alpha diversity boxplot?
alpha_diversity taxa ASV box_plot shannon
updated 16 months ago by • 0 • written 2.2 years ago by ▴ 180
4
votes
7
replies
3.1k
views
Error input data must be numeric in R, how to solve it?
error_numeric ASV_file R
2.2 years ago by Amr ▴ 180
0
votes
3
replies
1.5k
views
How to plot all enrichment plots from GSEA in one single plot in python or R?
R python ES GSEA
updated 2.1 years ago by 44k • written 2.2 years ago by ▴ 180
4
votes
7
replies
4.2k
views
Why we use adjusted p-value not p-value in differential gene expression analysis ?
p-value adjusted-p-value DGE DESeq2
2.2 years ago by Amr ▴ 180
0
votes
2
replies
779
views
Is there a setting in GSEA software to filter counts less than 10 before go for GSEA analysis?
GSEA
updated 2.2 years ago by ▴ 100 • written 2.3 years ago by ▴ 180
2
votes
1
reply
647
views
How to change the design DESeqDataSet to calculate log2foldChange in different way?
design DESeqDataSetFromMatrix condition DESeq2
2.2 years ago by Amr ▴ 180
0
votes
3
replies
1.5k
views
What is the best way to visualize the enrichment plots together after obtaining them from GSEA report?
ES enrichment_plot GSEA
updated 2.2 years ago by ★ 2.0k • written 2.2 years ago by ▴ 180
1
vote
1
reply
728
views
How to add color to specific groups of a boxplot in Python?
boxplot python pandas
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 180
1
vote
1
reply
937
views
Error in linear regression for multiple data-frames with matplotlib
linear_regression matplotlib
updated 2.3 years ago by 148k • written 2.3 years ago by ▴ 180
1
vote
2
replies
830
views
How to change values on X-axis in matplotlib ?
matplotlib python pandas
updated 2.3 years ago by 44k • written 2.3 years ago by ▴ 180
2
votes
6
replies
1.1k
views
How to add illustrative bar in ggplot2?
ggplot2 R
2.3 years ago by Amr ▴ 180
2
votes
10
replies
2.8k
views
R-studio freezes error
RStudio offtopic
updated 2.3 years ago by 44k • written 2.3 years ago by ▴ 180
2
votes
1
reply
643
views
What are the differences between significance, effect and standard deviation upon producing mitch reports?
R significance Standard-Deviation mitch
updated 4 months ago by 44k • written 2.3 years ago by ▴ 180
2
votes
1
reply
530
views
mitch report inquiries
mitch R
2.3 years ago by Amr ▴ 180
1
vote
3
replies
1.1k
views
How Wald test calculates p-values in DESeq2?
Wald p-value DESeq2
2.3 years ago by Amr ▴ 180
5
votes
2
replies
751
views
How to calculate effect size between two gene sets?
distance effectSize euclidean
updated 2.3 years ago by 148k • written 2.3 years ago by ▴ 180
2
votes
3
replies
811
views
Error in mitch in R
mitch symbols gene R
updated 2.3 years ago by 13k • written 2.3 years ago by ▴ 180
6
votes
5
replies
3.1k
views
How to select rows which has NA in any column in the dataframe in R?
dataframe NA R
updated 2.3 years ago by 13k • written 2.3 years ago by ▴ 180
0
votes
2
replies
661
views
Error in mitch reports in R
mitch R
updated 12 months ago by ★ 1.9k • written 2.3 years ago by ▴ 180
16
votes
8
replies
2.4k
views
6 follow
How to convert Ensemble Gene IDs to gene symbols or Entrez Gene IDs?
Gene Symbols mitch IDs
updated 2.3 years ago by 102k • written 2.3 years ago by ▴ 180
1
vote
8
replies
18k
views
How to update rlang in R?
rlang R
2.3 years ago by Amr ▴ 180
4
votes
4
replies
903
views
How to take data from dataframe to put it in another dataframe in R?
dataframe R
2.3 years ago by Amr ▴ 180
5
votes
9
replies
1.9k
views
Convert Gene Ensemble IDs to Gene Symbols on R
Ensemble R Gene-Symbols biomart
updated 19 months ago by 44k • written 2.3 years ago by ▴ 180
0
votes
1
reply
580
views
Depending on which counts number, the genes are overexpressed either up or down regulated in GSEA ?
gene GSEA geneset
updated 2.3 years ago by ★ 1.8k • written 2.3 years ago by ▴ 180
7
votes
2
replies
9.9k
views
How to use biomart on R to convert Ensembl Gene IDs to Symbols?
IDs R biomart Ensembl Symbols
updated 2.3 years ago by ★ 2.4k • written 2.3 years ago by ▴ 180
2
votes
2
replies
792
views
Why the number of genes decreased after dds (DESeqDataSetFromMatrix)?
R DESeq2
updated 15 months ago by 44k • written 2.3 years ago by ▴ 180
0
votes
3
replies
825
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 2.3 years ago by 102k • written 2.3 years ago by ▴ 180
2
votes
3
replies
915
views
How to shade columns for dataframe in ggplot that has 2 dataframes?
ggplot2 R
updated 2.3 years ago by 12k • written 2.3 years ago by ▴ 180
0
votes
1
reply
504
views
How to change colors for 1 data frame on a ggplot for combined 2 dataframes on R?
R dataframe ggplot
updated 2.3 years ago by ★ 1.8k • written 2.3 years ago by ▴ 180
3
votes
2
replies
726
views
Why we perform coldata dataframe in normalization with DESeq2 on R?
dataframe coldata DESeq2 normalization R GSEA
2.3 years ago by Amr ▴ 180
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