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240
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How can I get raw CPTAC protein quantification data ?
CPTAC proteomics proteins python transcriptome
8 weeks ago by AlexStar ▴ 170
0
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3
replies
436
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Understanding how to deal with Brain snRNA-seq data
scanpy python single-cell anndata RNA
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by ▴ 170
2
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5
replies
738
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snRNA-seq of the healthy human brain
python scanpy anndata single-cell
updated 3 months ago by 4.9k • written 3 months ago by ▴ 170
0
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4
replies
555
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Ontology for column naming in RNA-seq data
python scanpy anndata single-cell
updated 3 months ago by 150k • written 3 months ago by ▴ 170
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2
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464
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Help with finding scRNA-seq data
10x scanpy python single-cell anndata
4 months ago by AlexStar ▴ 170
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2
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845
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Using Tumor Immune Dysfunction and Exclusion (TIDE)
TPM cancer r
4 months ago by AlexStar ▴ 170
3
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1
reply
481
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What is the reason that all high throughput sequencing data for the human brain is snRNA-seq instead of scRNA-seq ?
10x scanpy python single-cell anndata
updated 4 months ago by ★ 18k • written 4 months ago by ▴ 170
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1
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314
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What are the epithelial cells subtype in esophagus tissue ?
python scanpy anndata single-cell
updated 5 months ago by 87k • written 5 months ago by ▴ 170
1
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7
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987
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How do decide if a processed scRNA-seq data is read counts or UMI format ?
scanpy python single-cell anndata RNA
updated 8 months ago by 87k • written 8 months ago by ▴ 170
2
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6
replies
956
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Finding scRNA-seq datasets of healthy human ovaries
python GEO single-cell RNA
updated 9 months ago by 45k • written 9 months ago by ▴ 170
1
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1
reply
903
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Reading files from different types as H5AD
python scanpy anndata single-cell
updated 9 months ago by ★ 3.0k • written 9 months ago by ▴ 170
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0
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287
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Empty kernel in SEACells model
single-cell scanpy seacells python anndata
10 months ago by AlexStar ▴ 170
0
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9
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1.8k
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 10 months ago by ★ 2.1k • written 10 months ago by ▴ 170
12
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7
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7.1k
views
6 follow
Convert FPKM to TPM in R
r TPM normalization meta-analysis
updated 13 months ago by 45k • written 2.5 years ago by ▴ 170
4
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10
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1.8k
views
6 follow
Deciding if a study used Bulk or single-cell RNA sequencing using the GEO data
GEO RNA-seq
updated 14 months ago by 45k • written 14 months ago by ▴ 170
6
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5
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1.3k
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Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 14 months ago by 89k • written 14 months ago by ▴ 170
1
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2
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654
views
What type of cancer did they study in this paper?
cancer RNAseq single-cell
updated 16 months ago by 150k • written 16 months ago by ▴ 170
0
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3
replies
806
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Discrepancies Between GEO Page and its article - Seeking Clarification
cancer GEO RNA-seq
updated 17 months ago by 45k • written 17 months ago by ▴ 170
1
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5
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7.4k
views
Code for reading h5ad files in R
r RNA-seq single-cell
updated 17 months ago by ★ 1.7k • written 17 months ago by ▴ 170
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8
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1.4k
views
Understaning the result of Meta-analysis of differential expression across datasets
r differential-expression genes
updated 19 months ago by 21k • written 19 months ago by ▴ 170
0
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1
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782
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Remove batch effects on the train set to avoid information leakage
r limma batch-effect
updated 19 months ago by 45k • written 19 months ago by ▴ 170
0
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11
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1.6k
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Performing differential expression analysis after applying transformations on my data
normalization differential-expression r
19 months ago by AlexStar ▴ 170
0
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1
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972
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How to tune and use the MetaVolcanoR
limma Bioconductor r MetaVolcanoR
updated 20 months ago by ★ 2.0k • written 2.6 years ago by ▴ 170
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4
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1.5k
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TPM normalization but library size isn't equal to 1 million
normalization TPM cancer r
updated 21 months ago by ★ 7.3k • written 21 months ago by ▴ 170
0
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5
replies
1.1k
views
Using IMmuno-PREdictive Score (IMPRES)
scaling TPM cancer normalization r
updated 21 months ago by 45k • written 21 months ago by ▴ 170
1
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1
reply
1.1k
views
Filtering genes after TPM normalization
filtering normalization TPM r
updated 21 months ago by ▴ 250 • written 21 months ago by ▴ 170
0
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2
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1.1k
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival cancer r
21 months ago by AlexStar ▴ 170
2
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3
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1.6k
views
What is the best way to clean bulk RNA-seq data?
normalization TPM r
updated 22 months ago by ★ 1.4k • written 22 months ago by ▴ 170
2
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3
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987
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What type of normalization did they use in this article?
normalization TPM r
updated 22 months ago by 45k • written 22 months ago by ▴ 170
0
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5
replies
1.5k
views
Is there anyway to cancel CPM normalization?
r TPM normalization
updated 22 months ago by 14k • written 23 months ago by ▴ 170
2
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1
reply
1.3k
views
Timeout error using Biomart to get gene lengths
r biomart
updated 2.1 years ago by 45k • written 2.1 years ago by ▴ 170
0
votes
1
reply
596
views
How to identify which are the the pre therapy samples?
data RNA-seq
updated 2.1 years ago by ★ 2.0k • written 2.1 years ago by ▴ 170
0
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2
replies
741
views
Where can I get the ICB datasets in this website?
data r ICB
updated 2.1 years ago by 150k • written 2.1 years ago by ▴ 170
0
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5
replies
1.2k
views
Check what are the columns that are enriched in each t-SNE cluster
r Dimensionality-reduction MachineLearning Rtsne
updated 2.2 years ago by ★ 29k • written 2.2 years ago by ▴ 170
0
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0
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668
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cutpointr package in R for finding the optimal cut of a predictive model
r ROC machine caret learning
2.3 years ago by AlexStar ▴ 170
1
vote
5
replies
2.4k
views
Is it adviced to remove genes with very low expression in TPM data?
r TPM RNA-seq clean
updated 2.4 years ago by 4.6k • written 2.4 years ago by ▴ 170
3
votes
1
reply
902
views
How to calculate the effictive gene length in R?
r TPM normalization
2.4 years ago by AlexStar ▴ 170
1
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2
replies
4.0k
views
Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : Gateway Timeout (HTTP 504).
r ensemble biomart
updated 2.4 years ago by ★ 2.1k • written 2.5 years ago by ▴ 170
0
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3
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3.0k
views
Understanding log2 transformation for TPM
r transformation TPM log2
updated 2.4 years ago by ★ 1.2k • written 2.5 years ago by ▴ 170
5
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1
reply
1.8k
views
argument ".f" is missing, with no default
r exons genes
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 170
2
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6
replies
1.3k
views
Batch effect correction with cell type enrichment analysis
limma RNA-seq r batch-effect
updated 11 months ago by 45k • written 2.5 years ago by ▴ 170
0
votes
1
reply
776
views
Comparing gene expression between two groups, using boxplots
r DEG TPM boxplot
2.6 years ago by AlexStar ▴ 170
1
vote
3
replies
770
views
TPM normalization result
normalization r TPM
updated 2.6 years ago by 4.9k • written 2.6 years ago by ▴ 170
2
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12
replies
3.9k
views
The best way to get gene lengths for 15K+ genes?
r EDAseq RNA-seq
2.5 years ago by AlexStar ▴ 170
0
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7
replies
2.7k
views
Warning - longer object length is not a multiple of shorter object length
genelength r TPM RNA-seq
updated 2.6 years ago by ★ 7.8k • written 2.6 years ago by ▴ 170
0
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0
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511
views
What does batch effect correction mean?
effects batch r data limma
2.7 years ago by AlexStar ▴ 170
0
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2
replies
1.0k
views
Error with TCGA package - TCGAbiolinks
TCGA r cancer
2.7 years ago by AlexStar ▴ 170
4
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6
replies
3.5k
views
ESTIMATE tumor purity
purity r cancer
2.7 years ago by AlexStar ▴ 170
0
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3
replies
1.1k
views
Searching for RNA-seq melanoma samples in TCGA or cBioPortal
TCGA r cBioPortal cancer
updated 2.7 years ago by ▴ 130 • written 2.7 years ago by ▴ 170
0
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1
reply
675
views
From counts to TPM code verification
TPM normalization r
updated 2.8 years ago by 87k • written 2.8 years ago by ▴ 170
68 results • Page 1 of 2
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