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3
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1.2k
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Answer: Answer: Good alignment rate for DNA-seq data
7 months ago by e.r.zakiev ▴ 210
0
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1
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605
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Comment: Comment: Cloud Computing w.r.t. AWS, Google Cloud, Microsoft Azure
7 months ago by e.r.zakiev ▴ 210
1
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0
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1.2k
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Comment: Comment: remove batch effect
7 months ago by e.r.zakiev ▴ 210
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0
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1.4k
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Comment: Comment: Why is chromHMM's binarizeBed with the -peaks argument not recommended for broad
8 months ago by e.r.zakiev ▴ 210
0
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0
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1.4k
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Comment: Comment: Extract RPKM values from Diffbind
8 months ago by e.r.zakiev ▴ 210
0
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1
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718
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
10 months ago by e.r.zakiev ▴ 210
0
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1
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718
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Comment: Comment: barcodes not show up in overrepresented sequences in FASTQC
10 months ago by e.r.zakiev ▴ 210
6
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5
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718
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barcodes not show up in overrepresented sequences in FASTQC
ribo-seq barcodes
updated 10 months ago by 142k • written 10 months ago by ▴ 210
0
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0
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637
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Answer: Answer: Where can I find a TF-target gene network for skin tissue
11 months ago by e.r.zakiev ▴ 210
0
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0
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484
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Comment: Comment: Panther db Reference List
11 months ago by e.r.zakiev ▴ 210
3
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2
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484
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Panther db Reference List
pantherdb enrichment-tests
updated 11 months ago by 43k • written 11 months ago by ▴ 210
3
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0
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638
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Answer: Answer: Sewage covid sequence analysis using C-Wap
12 months ago by e.r.zakiev ▴ 210
0
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0
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36k
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Comment: Comment: ATAC-seq peak calling with MACS
13 months ago by e.r.zakiev ▴ 210
3
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1
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477
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Why not use ONLY promoter-bound peaks when testing for enrichment in differentially-bound regions?
ChIP-seq ChIPseeker GO
updated 13 months ago by 43k • written 13 months ago by ▴ 210
2
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0
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2.8k
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Answer: Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
13 months ago by e.r.zakiev ▴ 210
0
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1
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2.8k
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Comment: Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
13 months ago by e.r.zakiev ▴ 210
0
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1
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1.4k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
14 months ago by e.r.zakiev ▴ 210
1
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0
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1.6k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
14 months ago by e.r.zakiev ▴ 210
0
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0
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1.6k
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Comment: Comment: Sorting a STAR-output bam file with samtools leads to a significant reduction in
14 months ago by e.r.zakiev ▴ 210
0
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0
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1.4k
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Comment: Comment: msigdbr returns the same genesets for mouse as in for human,
14 months ago by e.r.zakiev ▴ 210
0
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0
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5.8k
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Comment: Comment: Ensembl Hg38 dna, dna_rm, and dna_sm
14 months ago by e.r.zakiev ▴ 210
2
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5
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1.4k
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msigdbr returns the same genesets for mouse as in for human,
msigdbr
updated 14 months ago by 13k • written 14 months ago by ▴ 210
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0
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20k
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Comment: Comment: Cell Type Marker Databases?
14 months ago by e.r.zakiev ▴ 210
12
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8
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1.6k
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Sorting a STAR-output bam file with samtools leads to a significant reduction in size of the sorted bam file
samtools STAR
14 months ago by e.r.zakiev ▴ 210
0
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0
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11k
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Comment: Comment: How to submit multithreaded jobs on SLURM and determine number of threads?
14 months ago by e.r.zakiev ▴ 210
0
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0
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427
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Double-pass with STAR for better detection of spliced variants in assessing quality of FFPE RNAseq data: should I go for it?
RNA-seq STAR
updated 14 months ago by 43k • written 14 months ago by ▴ 210
0
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1
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2.5k
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Comment: Comment: Splice aware vs splice unaware aligners?
14 months ago by e.r.zakiev ▴ 210
0
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0
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44k
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Comment: Comment: Snakemake vs. Nextflow: strengths and weaknesses
14 months ago by e.r.zakiev ▴ 210
0
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0
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36k
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Comment: Comment: Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
14 months ago by e.r.zakiev ▴ 210
0
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1
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4.7k
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Comment: Comment: What does the decimal ending of a transcript id mean?
14 months ago by e.r.zakiev ▴ 210
3
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1
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691
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Which reference transcriptome/genome to use for mus musculus if I know the particular strain involved in the experiment?
mice alignment genome transcriptome
updated 14 months ago by 43k • written 14 months ago by ▴ 210
0
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0
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18k
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Comment: Comment: RNA-Seq analysis using STAR and Salmon
14 months ago by e.r.zakiev ▴ 210
0
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1
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1.5k
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Comment: Comment: Reference genome
14 months ago by e.r.zakiev ▴ 210
0
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0
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1.4k
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Comment: Comment: blast engine error empty blast query vector
15 months ago by e.r.zakiev ▴ 210
4
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1
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573
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TruSeq Illumina adapters are BLASTed with a high confidence to some genes/terms
RNAseq adapters Truseq BLAST
updated 15 months ago by 82k • written 15 months ago by ▴ 210
0
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0
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4.8k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
19 months ago by e.r.zakiev ▴ 210
0
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0
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4.8k
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Comment: Comment: Methodological problems are extremely common for enrichment analysis - beware th
19 months ago by e.r.zakiev ▴ 210
1
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0
replies
793
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Answer: Answer: Gene Rank for GSEA Preranked analysis?
19 months ago by e.r.zakiev ▴ 210
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