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0
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0
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194
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Differentiate sequenced and imputed variants in BGEN files
imputation bgen ukb
5 months ago by user230613 ▴ 360
0
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0
replies
332
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Calculating PRS from pre-computed PGS Catalog
GWAS PRS PGS
5 months ago by user230613 ▴ 360
10
votes
10
replies
5.2k
views
fgsea after deseq2, criteria for ranking DEGs.
GSEA
updated 22 months ago by 82k • written 22 months ago by ▴ 360
0
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0
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5.2k
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Comment: Comment: fgsea after deseq2, criteria for ranking DEGs.
22 months ago by user230613 ▴ 360
0
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1
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5.2k
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Comment: Comment: fgsea after deseq2, criteria for ranking DEGs.
22 months ago by user230613 ▴ 360
0
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1
reply
5.2k
views
Comment: Comment: fgsea after deseq2, criteria for ranking DEGs.
22 months ago by user230613 ▴ 360
0
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1
reply
23k
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Comment: Comment: Gene Set Enrichment Analysis
2.1 years ago by user230613 ▴ 360
0
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0
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1.2k
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Comment: Comment: lfcShrink MA plot comparison
2.1 years ago by user230613 ▴ 360
0
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1
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1.2k
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Comment: Comment: lfcShrink MA plot comparison
2.1 years ago by user230613 ▴ 360
0
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1
reply
1.2k
views
Comment: Comment: lfcShrink MA plot comparison
2.1 years ago by user230613 ▴ 360
2
votes
6
replies
1.2k
views
lfcShrink MA plot comparison
lfcShrink deseq2
updated 2.1 years ago by ★ 2.6k • written 2.1 years ago by ▴ 360
0
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1
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1.2k
views
Comment: C: convert CDS coordinates of a GTF to amino acid coordinates respect the resultant
3.7 years ago by user230613 ▴ 360
1
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3
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1.2k
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convert CDS coordinates of a GTF to amino acid coordinates respect the resultant protein
protein coordinates
3.7 years ago by user230613 ▴ 360
9
votes
9
replies
3.7k
views
Extract sequence number "X" from multifasta file
fasta
updated 2.1 years ago by 43k • written 9.4 years ago by ▴ 360
2
votes
3
replies
5.8k
views
CIRCOS plot with Chip-Seq Data
ChIP-Seq circos
updated 3.9 years ago by ★ 3.4k • written 8.7 years ago by ▴ 360
0
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1
reply
4.6k
views
Comment: C: promoter position estimation
updated 4.4 years ago by 43k • written 8.3 years ago by ▴ 360
0
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0
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34k
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Comment: A: Multi-Sample Vcf To Phylogenetic Tree.
updated 4.4 years ago by 43k • written 8.4 years ago by ▴ 360
21
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10
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16k
views
9 follow
Extract reads within given region, and their mates
bam samtools
updated 13 months ago by ▴ 20 • written 8.8 years ago by ▴ 360
4
votes
4
replies
5.1k
views
Does vcf-consensus support indels?
consensus vcf-consensus
updated 6.1 years ago by ▴ 70 • written 8.2 years ago by ▴ 360
0
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0
replies
13k
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Comment: C: Difference between the Fasta files from UCSC and Gencode/Ensembl
6.1 years ago by user230613 ▴ 360
0
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1
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1.8k
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Mate negative strand flag does not match read negative strand flag of mate
bam validatesamfile rnaseq
updated 6.3 years ago by 5.7k • written 6.3 years ago by ▴ 360
1
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1
reply
2.2k
views
consensus sequence of complex estructural variants
consensus estructural variant
updated 2.0 years ago by 43k • written 9.2 years ago by ▴ 360
0
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0
replies
5.7k
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Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
6.4 years ago by user230613 ▴ 360
6
votes
9
replies
9.6k
views
6 follow
Intersect multiple bed and keep all fields
bed bedtools bedops
updated 18 months ago by 43k • written 8.7 years ago by ▴ 360
0
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1
reply
5.7k
views
Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
6.5 years ago by user230613 ▴ 360
5
votes
1
reply
3.1k
views
GATK; Variant calling RNA-Seq best practices: bam processing steps
variant-calling RNA-Seq gatk
updated 6 months ago by 43k • written 6.6 years ago by ▴ 360
8
votes
4
replies
5.7k
views
TPM VS FPKM VS TMM and K-mer specific expression quantification
RNA-Seq kmer
updated 6.7 years ago by 6.5k • written 6.9 years ago by ▴ 360
0
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1
reply
1.5k
views
Comment: C: Specific sequence abundance using RNA-Seq
6.8 years ago by user230613 ▴ 360
3
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4
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1.5k
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Specific sequence abundance using RNA-Seq
expression RNA-Seq
updated 6.8 years ago by 20k • written 6.8 years ago by ▴ 360
0
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1
reply
21k
views
Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
6.9 years ago by user230613 ▴ 360
0
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1
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21k
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Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
6.9 years ago by user230613 ▴ 360
0
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0
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2.1k
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Comment: C: Subset of transcripts - Do I need to re-scale the TPM values?
6.9 years ago by user230613 ▴ 360
3
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3
replies
2.1k
views
Subset of transcripts - Do I need to re-scale the TPM values?
RNA-Seq tpm kallisto
6.9 years ago by user230613 ▴ 360
0
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1
reply
9.8k
views
Comment: C: kallisto: strand-specific and fragment length calculation
6.9 years ago by user230613 ▴ 360
7
votes
11
replies
9.8k
views
7 follow
kallisto: strand-specific and fragment length calculation
RNA-Seq kallisto
updated 7.0 years ago by ▴ 120 • written 7.0 years ago by ▴ 360
1
vote
3
replies
2.5k
views
bam-readcount tool: output zero coverage bases
bam-readcount
updated 7.0 years ago by 22k • written 7.1 years ago by ▴ 360
2
votes
8
replies
2.4k
views
samstat and samtools differ in the number of MAPQ=0 reads/alignments.
bwa samtools samstat
7.0 years ago by user230613 ▴ 360
0
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0
replies
2.5k
views
Comment: C: bam-readcount tool: output zero coverage bases
7.1 years ago by user230613 ▴ 360
0
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1
reply
2.4k
views
Comment: C: samstat and samtools differ in the number of MAPQ=0 reads/alignments.
7.1 years ago by user230613 ▴ 360
0
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1
reply
2.4k
views
Comment: C: samstat and samtools differ in the number of MAPQ=0 reads/alignments.
7.1 years ago by user230613 ▴ 360
0
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1
reply
2.4k
views
Comment: C: number of MAPQ=0 reads or alignments in BWA MEM output
7.1 years ago by user230613 ▴ 360
0
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0
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2.4k
views
Comment: C: samstat and samtools differ in the number of MAPQ=0 reads/alignments
7.1 years ago by user230613 ▴ 360
0
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1
reply
1.9k
views
Varscan2 filters AND usability of the tool - looking for opinions
varscan2 variant calling varscan somatic
7.1 years ago by user230613 ▴ 360
0
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1
reply
3.9k
views
Comment: C: WES reads mapping: RNASeq or DNASeq aligner?
7.2 years ago by user230613 ▴ 360
5
votes
4
replies
3.9k
views
WES reads mapping: RNASeq or DNASeq aligner?
mapping alignment wes
updated 7.2 years ago by ★ 2.8k • written 7.2 years ago by ▴ 360
7
votes
7
replies
6.5k
views
NGS data simulation: VarSim or BAMSurgeon?
simulation varsim bamsurgeon
updated 7.2 years ago by ★ 2.9k • written 7.2 years ago by ▴ 360
0
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0
replies
4.4k
views
Comment: C: SomaticSniper VS Varscan2
7.2 years ago by user230613 ▴ 360
5
votes
3
replies
4.4k
views
SomaticSniper VS Varscan2
varscan2 variant-calling somaticSniper
updated 6 months ago by 43k • written 7.2 years ago by ▴ 360
0
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1
reply
2.8k
views
rsem-calculate-expression prints out the help information when trying to run it
rsem
updated 7.4 years ago by 20 • written 7.5 years ago by ▴ 360
6
votes
4
replies
3.9k
views
GFF3 ID field: "Official" nomenclature
gff3
updated 7.7 years ago by 4.1k • written 8.1 years ago by ▴ 360
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