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6
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How different is rlog transformation from vst transformation in DESeq2
DESeq2 count normalization
updated 2.3 years ago by 90k • written 7.1 years ago by ▴ 710
1
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1.5k
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Comment: Comment: How to find DEG within a cluster between two groups without any replication info
3.4 years ago by piyushjo ▴ 710
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1
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1.5k
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Comment: Comment: How to find DEG within a cluster between two groups without any replication info
3.4 years ago by piyushjo ▴ 710
0
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0
replies
1.0k
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MACS2: broad and broad no-model output peaks are exactly the same. Is something wrong?
ChIP-seq macs2 H3K27ac
3.4 years ago by piyushjo ▴ 710
0
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1
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8.6k
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Answer: A: How to retrieve sets of protein sequences?
updated 5.1 years ago by 45k • written 6.9 years ago by ▴ 710
1
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1
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1.9k
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Comment: C: Is Pseudotime analysis most applicable to time-series experiments?
5.4 years ago by piyushjo ▴ 710
0
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0
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1.6k
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Comment: C: Advice for a start in Bioinformatics
5.5 years ago by piyushjo ▴ 710
1
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1
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3.5k
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Answer: A: pre-mRNA GTF reference for 10x
5.5 years ago by piyushjo ▴ 710
1
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1
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3.8k
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Comment: C: principal component analysis (PCA) of single cell samples which come from differ
5.5 years ago by piyushjo ▴ 710
1
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0
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3.8k
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Answer: A: principal component analysis (PCA) of single cell samples which come from differ
5.5 years ago by piyushjo ▴ 710
1
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0
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3.0k
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Comment: C: Compare signatures between scRNA-seq clusters in R
5.5 years ago by piyushjo ▴ 710
0
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0
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1.0k
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Comment: C: Tophat / output without XS
5.5 years ago by piyushjo ▴ 710
1
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0
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5.2k
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Comment: C: Recommendation for packages for cell type deconvolution from bulk RNAseq data?
5.5 years ago by piyushjo ▴ 710
1
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1
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3.2k
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Comment: C: PCA on FPKM data
5.5 years ago by piyushjo ▴ 710
0
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0
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3.2k
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Comment: C: WGCNA "trait" file format?
5.5 years ago by piyushjo ▴ 710
1
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1
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3.2k
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Answer: C: PCA on FPKM data
5.5 years ago by piyushjo ▴ 710
0
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2
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3.2k
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Comment: C: WGCNA "trait" file format?
5.5 years ago by piyushjo ▴ 710
0
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1
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3.2k
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Comment: C: WGCNA "trait" file format?
5.5 years ago by piyushjo ▴ 710
0
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0
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1.1k
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Comment: C: Classification of long non-coding RNAs
5.5 years ago by piyushjo ▴ 710
2
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0
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15k
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Comment: C: Rename Idents in Seurat Object
5.5 years ago by piyushjo ▴ 710
2
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0
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1.7k
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Comment: C: Raw Data Requirement for RNA-Seq paper submission
5.5 years ago by piyushjo ▴ 710
1
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0
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4.8k
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Comment: C: Batch correction in scRNA-seq data via fastMNN | pro/contra
5.5 years ago by piyushjo ▴ 710
1
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0
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4.7k
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Comment: C: Have we failed as bioinformatician in this time of COVID-19
5.5 years ago by piyushjo ▴ 710
0
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0
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27k
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Comment: C: ggplot2 labeling and coloring specific Data points in Scatter Plot
5.5 years ago by piyushjo ▴ 710
0
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1
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3.5k
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Comment: C: Optimal K-means cluster # for large data (R)
5.5 years ago by piyushjo ▴ 710
0
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0
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2.9k
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Comment: C: Deseq2 design matrix for multiple factors
5.5 years ago by piyushjo ▴ 710
0
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1
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3.5k
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Answer: C: Optimal K-means cluster # for large data (R)
5.5 years ago by piyushjo ▴ 710
1
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0
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1.3k
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Comment: C: Seurat code availability for published papers
5.5 years ago by piyushjo ▴ 710
0
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0
replies
1.5k
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Comment: C: DESeq analysis with different replication
5.5 years ago by piyushjo ▴ 710
0
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0
replies
1.4k
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Comment: C: Marker genes of a scRNA-Seq experiment not found in the processed data set gene
5.5 years ago by piyushjo ▴ 710
0
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1
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1.4k
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Comment: C: Marker genes of a scRNA-Seq experiment not found in the processed data set gene
5.5 years ago by piyushjo ▴ 710
0
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1
reply
2.2k
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Comment: C: How to best summarize read counts overlapping promoters when read counts are def
5.5 years ago by piyushjo ▴ 710
0
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0
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1.5k
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Comment: C: How to distinguish malignant vs non-malignant cells based on gene expression dat
5.5 years ago by piyushjo ▴ 710
0
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1
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1.5k
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Comment: C: How to distinguish malignant vs non-malignant cells based on gene expression dat
5.5 years ago by piyushjo ▴ 710
0
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0
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2.1k
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Answer: A: How to map find specific genes in RNA Seq dataset ?
5.5 years ago by piyushjo ▴ 710
1
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1
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2.1k
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Comment: C: How to map find specific genes in RNA Seq dataset ?
5.5 years ago by piyushjo ▴ 710
1
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1
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2.1k
views
Comment: C: How to map find specific genes in RNA Seq dataset ?
5.5 years ago by piyushjo ▴ 710
1
vote
1
reply
2.1k
views
Comment: C: How to map find specific genes in RNA Seq dataset ?
5.5 years ago by piyushjo ▴ 710
12
votes
3
replies
6.0k
views
How to make an intronic GTF for alignment
RNA-Seq intronic-gtf
updated 2.4 years ago by 45k • written 5.5 years ago by ▴ 710
1
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0
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6.0k
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Comment: C: How to make an intronic GTF for alignment
5.5 years ago by piyushjo ▴ 710
1
vote
0
replies
938
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Comment: C: Cannot find a gene in the counts table
5.5 years ago by piyushjo ▴ 710
2
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0
replies
25k
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Comment: C: Subsetting - Raw Counts from Seurat Object
5.5 years ago by piyushjo ▴ 710
0
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1
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25k
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Comment: C: Subsetting - Raw Counts from Seurat Object
5.5 years ago by piyushjo ▴ 710
1
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0
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3.0k
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Comment: C: STAR genome index Error
5.6 years ago by piyushjo ▴ 710
0
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1
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3.0k
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Comment: C: STAR genome index Error
5.6 years ago by piyushjo ▴ 710
0
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1
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3.0k
views
Comment: C: STAR genome index Error
5.6 years ago by piyushjo ▴ 710
0
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0
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11k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
5.6 years ago by piyushjo ▴ 710
1
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0
replies
11k
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Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
5.6 years ago by piyushjo ▴ 710
0
votes
1
reply
11k
views
Comment: C: Only doing log2 transformation for RNAseq read count data without normalizing by
5.6 years ago by piyushjo ▴ 710
2
votes
0
replies
2.0k
views
Comment: C: Consensus WGCNA: soft-threshold power selection
5.6 years ago by piyushjo ▴ 710
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