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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
0
votes
1
reply
883
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Comment: Comment: Deciding if a study used Bulk or single-cell RNA sequencing using the GEO data
3 months ago by JACKY ▴ 140
0
votes
0
replies
883
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Comment: Comment: Deciding if a study used Bulk or single-cell RNA sequencing using the GEO data
3 months ago by JACKY ▴ 140
6
votes
5
replies
706
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
392
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
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1
reply
525
views
Comment: Comment: Discrepancies Between GEO Page and its article - Seeking Clarification
6 months ago by JACKY ▴ 140
0
votes
3
replies
525
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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
1
reply
2.5k
views
Comment: Comment: Code for reading h5ad files in R
6 months ago by JACKY ▴ 140
0
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1
reply
2.5k
views
Comment: Comment: Code for reading h5ad files in R
6 months ago by JACKY ▴ 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
1
reply
948
views
Comment: Comment: Understaning the result of Meta-analysis of differential expression across datas
8 months ago by JACKY ▴ 140
0
votes
1
reply
948
views
Comment: Comment: Understaning the result of Meta-analysis of differential expression across datas
8 months ago by JACKY ▴ 140
0
votes
0
replies
948
views
Comment: Comment: Understaning the result of Meta-analysis of differential expression across datas
8 months ago by JACKY ▴ 140
0
votes
8
replies
948
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
0
replies
1.1k
views
Comment: Comment: Performing differential expression analysis after applying transformations on my
8 months ago by JACKY ▴ 140
0
votes
1
reply
1.1k
views
Comment: Comment: Performing differential expression analysis after applying transformations on my
8 months ago by JACKY ▴ 140
0
votes
1
reply
1.1k
views
Comment: Comment: Performing differential expression analysis after applying transformations on my
8 months ago by JACKY ▴ 140
0
votes
1
reply
1.1k
views
Comment: Comment: Performing differential expression analysis after applying transformations on my
8 months ago by JACKY ▴ 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
1.1k
views
Comment: Comment: Performing differential expression analysis after applying transformations on my
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
0
votes
0
replies
956
views
Comment: Comment: TPM normalization but library size isn't equal to 1 million
10 months ago by JACKY ▴ 140
1
vote
4
replies
956
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
1
reply
738
views
Comment: Comment: Using IMmuno-PREdictive Score (IMPRES)
10 months ago by JACKY ▴ 140
0
votes
1
reply
738
views
Comment: Comment: Using IMmuno-PREdictive Score (IMPRES)
10 months ago by JACKY ▴ 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
0
replies
735
views
Comment: Comment: What does "OS_CNSR" and "PFS_CNSR" mean?
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
0
votes
1
reply
609
views
Comment: Comment: What type of normalization did they use in this article?
11 months ago by JACKY ▴ 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
1
reply
1.1k
views
Comment: Comment: Is there anyway to cancel CPM normalization?
11 months ago by JACKY ▴ 140
0
votes
1
reply
1.1k
views
Comment: Comment: Is there anyway to cancel CPM normalization?
12 months ago by JACKY ▴ 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
1
reply
819
views
Comment: Comment: Check what are the columns that are enriched in each t-SNE cluster
15 months ago by JACKY ▴ 140
0
votes
1
reply
819
views
Comment: Comment: Check what are the columns that are enriched in each t-SNE cluster
15 months ago by JACKY ▴ 140
0
votes
5
replies
819
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
0
votes
0
replies
1.8k
views
Comment: Comment: Is it adviced to remove genes with very low expression in TPM data?
18 months ago by JACKY ▴ 140
0
votes
1
reply
1.8k
views
Comment: Comment: Is it adviced to remove genes with very low expression in TPM data?
18 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
561
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
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