Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
12
votes
7
replies
4.0k
views
6 follow
Convert FPKM to TPM in R
r TPM normalization meta-analysis
updated 9 weeks ago by 43k • written 19 months ago by ▴ 140
4
votes
10
replies
883
views
6 follow
Deciding if a study used Bulk or single-cell RNA sequencing using the GEO data
GEO RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 140
6
votes
5
replies
705
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 4 months ago by 87k • written 4 months ago by ▴ 140
1
vote
2
replies
391
views
What type of cancer did they study in this paper?
cancer RNAseq single-cell
updated 5 months ago by 142k • written 5 months ago by ▴ 140
0
votes
3
replies
524
views
Discrepancies Between GEO Page and its article - Seeking Clarification
cancer GEO RNA-seq
updated 6 months ago by 43k • written 6 months ago by ▴ 140
1
vote
5
replies
2.5k
views
Code for reading h5ad files in R
r RNA-seq single-cell
updated 6 months ago by ★ 1.6k • written 6 months ago by ▴ 140
0
votes
8
replies
944
views
Understaning the result of Meta-analysis of differential expression across datasets
r differential-expression genes
updated 8 months ago by 19k • written 8 months ago by ▴ 140
0
votes
1
reply
551
views
Remove batch effects on the train set to avoid information leakage
r limma batch-effect
updated 8 months ago by 43k • written 8 months ago by ▴ 140
0
votes
11
replies
1.1k
views
Performing differential expression analysis after applying transformations on my data
normalization differential-expression r
8 months ago by JACKY ▴ 140
0
votes
1
reply
683
views
How to tune and use the MetaVolcanoR
limma Bioconductor r MetaVolcanoR
updated 10 months ago by ★ 2.0k • written 20 months ago by ▴ 140
1
vote
4
replies
955
views
TPM normalization but library size isn't equal to 1 million
normalization TPM cancer r
updated 10 months ago by ★ 6.0k • written 10 months ago by ▴ 140
0
votes
5
replies
738
views
Using IMmuno-PREdictive Score (IMPRES)
scaling TPM cancer normalization r
updated 10 months ago by 43k • written 10 months ago by ▴ 140
1
vote
1
reply
671
views
Filtering genes after TPM normalization
filtering normalization TPM r
updated 11 months ago by ▴ 230 • written 11 months ago by ▴ 140
0
votes
0
replies
397
views
Using Tumor Immune Dysfunction and Exclusion (TIDE)
TPM cancer r
11 months ago by JACKY ▴ 140
0
votes
2
replies
735
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival cancer r
11 months ago by JACKY ▴ 140
2
votes
3
replies
1.0k
views
What is the best way to clean bulk RNA-seq data?
normalization TPM r
updated 11 months ago by ▴ 900 • written 11 months ago by ▴ 140
2
votes
3
replies
609
views
What type of normalization did they use in this article?
normalization TPM r
updated 11 months ago by 43k • written 11 months ago by ▴ 140
0
votes
5
replies
1.1k
views
Is there anyway to cancel CPM normalization?
r TPM normalization
updated 11 months ago by 14k • written 12 months ago by ▴ 140
2
votes
1
reply
925
views
Timeout error using Biomart to get gene lengths
r biomart
updated 14 months ago by 43k • written 14 months ago by ▴ 140
0
votes
1
reply
412
views
How to identify which are the the pre therapy samples?
data RNA-seq
updated 14 months ago by ★ 2.0k • written 14 months ago by ▴ 140
0
votes
2
replies
537
views
Where can I get the ICB datasets in this website?
data r ICB
updated 15 months ago by 142k • written 15 months ago by ▴ 140
0
votes
5
replies
818
views
Check what are the columns that are enriched in each t-SNE cluster
r Dimensionality-reduction MachineLearning Rtsne
updated 15 months ago by ★ 27k • written 15 months ago by ▴ 140
0
votes
0
replies
463
views
cutpointr package in R for finding the optimal cut of a predictive model
r ROC machine caret learning
17 months ago by JACKY ▴ 140
1
vote
5
replies
1.8k
views
Is it adviced to remove genes with very low expression in TPM data?
r TPM RNA-seq clean
updated 18 months ago by 4.2k • written 18 months ago by ▴ 140
3
votes
1
reply
560
views
How to calculate the effictive gene length in R?
r TPM normalization
18 months ago by JACKY ▴ 140
1
vote
2
replies
3.0k
views
Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : Gateway Timeout (HTTP 504).
r ensemble biomart
updated 18 months ago by ★ 2.0k • written 19 months ago by ▴ 140
0
votes
3
replies
2.0k
views
Understanding log2 transformation for TPM
r transformation TPM log2
updated 18 months ago by ★ 1.2k • written 19 months ago by ▴ 140
5
votes
1
reply
1.3k
views
argument ".f" is missing, with no default
r exons genes
updated 19 months ago by 13k • written 19 months ago by ▴ 140
2
votes
6
replies
882
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 19 days ago by 43k • written 19 months ago by ▴ 140
0
votes
1
reply
532
views
Comparing gene expression between two groups, using boxplots
r DEG TPM boxplot
20 months ago by JACKY ▴ 140
1
vote
3
replies
589
views
TPM normalization result
normalization r TPM
updated 20 months ago by 3.9k • written 20 months ago by ▴ 140
2
votes
12
replies
2.6k
views
The best way to get gene lengths for 15K+ genes?
r EDAseq RNA-seq
19 months ago by JACKY ▴ 140
0
votes
7
replies
2.0k
views
Warning - longer object length is not a multiple of shorter object length
genelength r TPM RNA-seq
updated 20 months ago by ★ 7.1k • written 21 months ago by ▴ 140
0
votes
0
replies
371
views
What does batch effect correction mean?
effects batch r data limma
21 months ago by JACKY ▴ 140
0
votes
2
replies
758
views
Error with TCGA package - TCGAbiolinks
TCGA r cancer
22 months ago by JACKY ▴ 140
4
votes
6
replies
1.9k
views
ESTIMATE tumor purity
purity r cancer
22 months ago by JACKY ▴ 140
0
votes
3
replies
766
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA r cBioPortal cancer
updated 21 months ago by ▴ 120 • written 22 months ago by ▴ 140
0
votes
1
reply
514
views
From counts to TPM code verification
TPM normalization r
updated 23 months ago by 82k • written 23 months ago by ▴ 140
0
votes
7
replies
1.3k
views
A check over my code using Limma DE, starting from normalized data
limma r
updated 19 months ago by ★ 7.1k • written 23 months ago by ▴ 140
1
vote
4
replies
1.1k
views
Cellular deconvolution does not work without batch effect correction
batch effect r deconvolution
updated 2.1 years ago by 82k • written 2.1 years ago by ▴ 140
0
votes
3
replies
1.1k
views
Error: Application depends on package "rlang" but it is not installed
shiny R
updated 2.1 years ago by 27k • written 2.1 years ago by ▴ 140
0
votes
0
replies
336
views
How to check if genes are important in cancer, using depmap or cBioPortal?
cBioPortal r depmap
2.1 years ago by JACKY ▴ 140
0
votes
2
replies
530
views
associate EBV to cancer
EBV r depmap
2.1 years ago by JACKY ▴ 140
0
votes
2
replies
756
views
low counts in DESeq2
DESeq2 r
2.1 years ago by JACKY ▴ 140
0
votes
5
replies
909
views
How to deal with batch effects of multiple datasets?
DESeq2 r
updated 2.1 years ago by 14k • written 2.2 years ago by ▴ 140
0
votes
0
replies
319
views
Primary and Metastatic genes
cancer DESeq2
2.2 years ago by JACKY ▴ 140
1
vote
7
replies
1.8k
views
Linear regression on RNA-seq data
r regression
2.2 years ago by JACKY ▴ 140
0
votes
0
replies
378
views
Contrast for LIMMA
r limma
2.2 years ago by JACKY ▴ 140
1
vote
8
replies
3.8k
views
limma - voom with TPM data
r limma
2.2 years ago by JACKY ▴ 140
0
votes
5
replies
2.4k
views
DESeq2 shrinking log fold-change
DESeq2 r
updated 2.2 years ago by ★ 2.6k • written 2.2 years ago by ▴ 140
56 results • Page 1 of 2
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6