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0
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2
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1.2k
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Pathways visualization as network
cytoscape Pathways
updated 3.8 years ago by ▴ 10 • written 3.8 years ago by ▴ 190
8
votes
9
replies
4.6k
views
Can we combine adjacent peaks in ATAC-Seq data
sequencing
updated 3.4 years ago by 89k • written 6.3 years ago by ▴ 190
1
vote
1
reply
1.7k
views
Regressing on cell cycle genes in scRNA-Seq
rna-seq single-cell
5.6 years ago by oriolebaltimore ▴ 190
2
votes
0
replies
7.1k
views
Answer: A: Aggregating Gene Expression Across Rows
updated 5.7 years ago by 45k • written 9.7 years ago by ▴ 190
3
votes
4
replies
2.3k
views
Given a bed file with range of peaks, is it possible to identify the summit of the peak
RNA-Seq
updated 6.2 years ago by 36k • written 6.2 years ago by ▴ 190
1
vote
0
replies
2.3k
views
Answer: A: Given a bed file with range of peaks, is it possible to identify the summit of t
6.2 years ago by oriolebaltimore ▴ 190
1
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1
reply
4.6k
views
Comment: A: Can we combine adjacent peaks in ATAC-Seq fata
6.2 years ago by oriolebaltimore ▴ 190
2
votes
1
reply
4.6k
views
Answer: A: Can we combine adjacent peaks in ATAC-Seq fata
6.2 years ago by oriolebaltimore ▴ 190
0
votes
2
replies
4.6k
views
Comment: A: Can we combine adjacent peaks in ATAC-Seq fata
6.3 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
2.5k
views
GSVA for mouse scRNA-Seq
scRNA-Seq GSVA
6.4 years ago by oriolebaltimore ▴ 190
5
votes
8
replies
6.8k
views
Identify reads that span intron-exon junctions in RNA-Seq
RNA-Seq
updated 6.5 years ago by ★ 1.5k • written 7.2 years ago by ▴ 190
0
votes
1
reply
26k
views
Answer: A: htseq-counts output merge into one matrix ??
6.6 years ago by oriolebaltimore ▴ 190
2
votes
1
reply
2.8k
views
When to remove duplicates using deduplication in Exome-Seq
TruSeq Exome-Seq DNA-Seq TrueSeq GATK
updated 6.7 years ago by 8.3k • written 6.7 years ago by ▴ 190
8
votes
6
replies
10k
views
Bigwig format and operation
Bigwig ChIP-Seq ATAC-Seq BigWig
6.8 years ago by oriolebaltimore ▴ 190
0
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0
replies
10k
views
Comment: A: Bigwig format and operation
6.8 years ago by oriolebaltimore ▴ 190
0
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0
replies
10k
views
Comment: C: Bigwig format and operation
6.8 years ago by oriolebaltimore ▴ 190
0
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1
reply
6.4k
views
Comment: A: bigWig to bed for regions above/below threshold
6.8 years ago by oriolebaltimore ▴ 190
0
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0
replies
10k
views
Comment: C: Bigwig format and operation
6.8 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
7.0k
views
Comment: A: How to fix .bam file that was diagnosed as "MISSING_READ_GROUP" by Picard Valida
updated 7.0 years ago by 153k • written 7.0 years ago by ▴ 190
0
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0
replies
6.8k
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Comment: A: Identify reads that span intron-exon junctions in RNA-Seq
7.0 years ago by oriolebaltimore ▴ 190
3
votes
1
reply
1.8k
views
TCGA data on cloud
RNA-Seq TCGA cloud computing
updated 7.0 years ago by ▴ 390 • written 7.0 years ago by ▴ 190
0
votes
1
reply
1.3k
views
Map XLOCs in cufflinks assembly GTF to genes
RNA-Seq
7.1 years ago by oriolebaltimore ▴ 190
0
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0
replies
8.8k
views
Comment: C: Empty output from MACS2 when using control
7.2 years ago by oriolebaltimore ▴ 190
0
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0
replies
6.8k
views
Comment: C: Identify reads that span intron-exon junctions in RNA-Seq
7.2 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
8.8k
views
Answer: A: Empty output from MACS2 when using control
7.2 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
2.8k
views
Comment: A: Mapping and annotating DNA binding regions from ChIP-Seq to nearby gene
7.2 years ago by oriolebaltimore ▴ 190
4
votes
4
replies
2.8k
views
Mapping and annotating DNA binding regions from ChIP-Seq to nearby gene
ChIP-Seq annotation
7.2 years ago by oriolebaltimore ▴ 190
3
votes
1
reply
3.2k
views
sigclust in Verhaak GBM cancer cell 2010
sigclust R
updated 7.5 years ago by ▴ 20 • written 8.7 years ago by ▴ 190
0
votes
3
replies
1.8k
views
HTSeq-count ambiguous results - all transcripts vs. single transcript
RNA-Seq HTSeq gene
7.5 years ago by oriolebaltimore ▴ 190
0
votes
2
replies
1.8k
views
Comment: A: HTSeq-count ambiguous results - all transcripts vs. single transcript
7.5 years ago by oriolebaltimore ▴ 190
5
votes
4
replies
11k
views
ssGSEA on RNA-Seq data from TCGA
RNA-Seq gene
updated 3.1 years ago by 45k • written 9.7 years ago by ▴ 190
4
votes
4
replies
5.2k
views
filter BAM file for reads that map 100% identity
samtools bam CIGAR
updated 2.8 years ago by ▴ 150 • written 7.8 years ago by ▴ 190
0
votes
1
reply
114k
views
Comment: A: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
8.3 years ago by oriolebaltimore ▴ 190
0
votes
0
replies
1.5k
views
how not to enforce FDR cutoff on cuffdiff result
RNA-Seq cuffdiff
8.5 years ago by oriolebaltimore ▴ 190
2
votes
1
reply
3.9k
views
VarScan for tumor only files
sequence alignment next-gen SNP
8.5 years ago by oriolebaltimore ▴ 190
0
votes
2
replies
1.7k
views
how to find if an observed missense SNV is true observation and significant in targeted sequencing of few (5 or less) genes.
next-gen sequencing targeted panels mutations
updated 8.5 years ago by 20 • written 8.7 years ago by ▴ 190
1
vote
0
replies
1.7k
views
Mutation calling rules in TCGA
variant calling
8.6 years ago by oriolebaltimore ▴ 190
0
votes
0
replies
2.2k
views
Given a bam file, obtain read numbers that traverse a specific exon junction
RNA-Seq alternative splicing
8.7 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
8.9k
views
Comment: C: RNA-Seq raw fastq files from TCGA
8.7 years ago by oriolebaltimore ▴ 190
3
votes
4
replies
8.9k
views
RNA-Seq raw fastq files from TCGA
RNA-Seq TCGA fastq
8.7 years ago by oriolebaltimore ▴ 190
0
votes
1
reply
2.9k
views
Cuffmerge and cuffdiff on bam file generated by STAR alignment
alignment cuffdiff star
8.7 years ago by oriolebaltimore ▴ 190
1
vote
5
replies
2.7k
views
RNA-Seq single end 50 bp - will tophat Cufflinks/cuffdiff work for differential expression
RNA-Seq cufflinks cuffdiff single-end 50bp
8.7 years ago by oriolebaltimore ▴ 190
0
votes
2
replies
2.7k
views
Comment: A: RNA-Seq single end 50 bp - will tophat Cufflinks/cuffdiff work for differential
8.7 years ago by oriolebaltimore ▴ 190
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