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Comment: Comment: counts of cite-seq-count vs. cellrenager varies tremendously
9 months ago by John Ma ▴ 310
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1
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1.5k
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Comment: Comment: counts of cite-seq-count vs. cellrenager varies tremendously
9 months ago by John Ma ▴ 310
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0
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912
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Answer: Answer: integrate single cell RNA sequencing data
10 months ago by John Ma ▴ 310
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2
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1.9k
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Comment: Comment: Counting intronic reads in bulk RNA-seq
10 months ago by John Ma ▴ 310
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6
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1.9k
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Counting intronic reads in bulk RNA-seq
rna-seq
updated 10 months ago by 14k • written 11 months ago by ▴ 310
0
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1
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2.4k
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Answer: Answer: Batch effect in integrated RNA-seq analysis
13 months ago by John Ma ▴ 310
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964
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Comment: Comment: Which to learn: TensorFlow or PyTorch?
2.1 years ago by John Ma ▴ 310
2
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3
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964
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Which to learn: TensorFlow or PyTorch?
PyTorch machine-learning TensorFlow deep-learning
2.1 years ago by John Ma ▴ 310
1
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0
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3.6k
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Answer: A: Narrow & Broad peaks from 'macs2 bdgdiff'
5.2 years ago by John Ma ▴ 310
1
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1
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1.3k
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Does a no-normal pipeline exist for MuSiC?
MuSiC
5.8 years ago by John Ma ▴ 310
0
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0
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928
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How likely do cDNAs with start-loss variants appear in mRNA-seq?
RNA-Seq rna-seq
6.4 years ago by John Ma ▴ 310
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1
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2.2k
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Comment: C: Strategies to call variants from a cancer sample
6.4 years ago by John Ma ▴ 310
3
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7
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2.2k
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Strategies to call variants from a cancer sample
SNP next-gen
updated 6.4 years ago by ★ 2.9k • written 6.4 years ago by ▴ 310
0
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0
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2.2k
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Comment: C: Strategies to call variants from a cancer sample
6.4 years ago by John Ma ▴ 310
0
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1
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2.2k
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Comment: C: Strategies to call variants from a cancer sample
6.4 years ago by John Ma ▴ 310
1
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0
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4.8k
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Comment: C: Mapping between genomic coordinates to transcriptomic coordinates
6.4 years ago by John Ma ▴ 310
1
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1
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10k
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Answer: A: ssGSEA on RNA-Seq data from TCGA
6.4 years ago by John Ma ▴ 310
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3
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2.8k
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How to get sequencing depths from VCF with Rsamtools
R pindel Rsamtools
updated 6.8 years ago by 161k • written 6.8 years ago by ▴ 310
0
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0
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2.8k
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Comment: C: How to get sequencing depths from VCF with Rsamtools
6.8 years ago by John Ma ▴ 310
0
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1
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4.3k
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
6.8 years ago by John Ma ▴ 310
1
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1
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4.3k
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
6.8 years ago by John Ma ▴ 310
1
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1
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4.3k
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Comment: C: bcftools: how to annotate a file with a larger file using bcftools annotate?
6.8 years ago by John Ma ▴ 310
1
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0
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4.3k
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Answer: A: bcftools: how to annotate a file with a larger file using bcftools annotate?
6.8 years ago by John Ma ▴ 310
0
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0
replies
1.1k
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Search VCF by ID in Python
SNP python
6.8 years ago by John Ma ▴ 310
0
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0
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2.6k
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Comment: C: Converting MuTect v1 text outputs to VCF
6.9 years ago by John Ma ▴ 310
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3
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2.6k
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Converting MuTect v1 text outputs to VCF
snp MuTect VCF
6.9 years ago by John Ma ▴ 310
1
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1
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2.6k
views
Answer: A: Converting MuTect v1 text outputs to VCF
6.9 years ago by John Ma ▴ 310
2
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0
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5.0k
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Answer: A: Ensembl ID differences between assemblies?
6.9 years ago by John Ma ▴ 310
2
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1
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2.2k
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Comment: C: Best pipeline for DE study
6.9 years ago by John Ma ▴ 310
0
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0
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2.2k
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Comment: C: Best pipeline for DE study
6.9 years ago by John Ma ▴ 310
3
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1
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2.2k
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Answer: A: Best pipeline for DE study
6.9 years ago by John Ma ▴ 310
0
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0
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5.2k
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Comment: C: How to convert vcf file into data matrix for machine-learning?
6.9 years ago by John Ma ▴ 310
4
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5
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4.8k
views
Mapping between genomic coordinates to transcriptomic coordinates
vcf gff gtf SNP
updated 6.9 years ago by ★ 3.8k • written 7.0 years ago by ▴ 310
1
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0
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4.8k
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Answer: A: Mapping between genomic coordinates to transcriptomic coordinates
6.9 years ago by John Ma ▴ 310
0
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1
reply
5.2k
views
Comment: C: How to convert vcf file into data matrix for machine-learning?
6.9 years ago by John Ma ▴ 310
2
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1
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5.2k
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Answer: A: How to convert vcf file into data matrix for machine-learning?
6.9 years ago by John Ma ▴ 310
1
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0
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1.7k
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Answer: A: Which package is appropriate to the normalised RNA-seq data for differential exp
6.9 years ago by John Ma ▴ 310
1
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0
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1.6k
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Answer: A: RNA-Seq pipeline for clustering
6.9 years ago by John Ma ▴ 310
3
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1
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4.0k
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Answer: A: Different results with edgeR when adding gene symbols
7.0 years ago by John Ma ▴ 310
2
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1
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3.6k
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Answer: C: I get the same modules but different number of genes WGCNA
7.0 years ago by John Ma ▴ 310
0
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0
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1.9k
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Answer: A: How many samples ones need to get a high power with RNA-Seq in paired-design exp
7.0 years ago by John Ma ▴ 310
1
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1
reply
1.6k
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TFBS ChIP-Seq: No Cross-correlation Peaks other than Read Length: Is it normal?
ChIP-Seq
updated 7.1 years ago by 104k • written 7.1 years ago by ▴ 310
0
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1
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5.5k
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Comment: C: Is log-transformation needed to calculate Euclidean distance metric from FPKM/TP
7.1 years ago by John Ma ▴ 310
4
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4
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5.5k
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Is log-transformation needed to calculate Euclidean distance metric from FPKM/TPM?
RNA-Seq clustering distance metric FPKM TPM
updated 7.2 years ago by ★ 2.8k • written 7.2 years ago by ▴ 310
4
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1
reply
2.3k
views
Adding Coverage Stats into MuTect2 output VCFs
sequencing SNP
updated 7.8 years ago by ▴ 100 • written 7.9 years ago by ▴ 310
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