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33
votes
30
replies
35k
views
9 follow
Converting Bam To Bedgraph For Viewing On Ucsc?
bedtools bam bed ucsc genome-browser
updated 3.5 years ago by ★ 1.7k • written 12.2 years ago by ▴ 960
2
votes
5
replies
6.3k
views
Adding Introns To Gff3 Format?
coordinates gff3 conversion
updated 3.8 years ago by 45k • written 12.2 years ago by ▴ 960
5
votes
8
replies
8.1k
views
Strandedness Of Homer For Motif Analysis
motif motif sequence
updated 7.3 years ago by 20 • written 12.2 years ago by ▴ 960
8
votes
2
replies
4.2k
views
Finding Gff File For All Uniprot Protein Isoform Domain Annotations
protein
updated 3.2 years ago by 45k • written 12.7 years ago by ▴ 960
10
votes
6
replies
11k
views
Gene set enrichment tool for RNA-Seq in Python?
gsea gene-ontology go RNA-Seq python
updated 9.0 years ago by ▴ 380 • written 11.0 years ago by ▴ 960
11
votes
2
replies
9.0k
views
How To Find Sample Information From Srr Labels In Geo?
geo illumina sra next-gen-sequencing
updated 2.2 years ago by 45k • written 11.8 years ago by ▴ 960
4
votes
4
replies
7.7k
views
Trouble Compiling C++ Code With Bamtools
samtools rna-seq
updated 9.4 years ago by • 0 • written 11.2 years ago by ▴ 960
1
vote
5
replies
5.4k
views
Tophat Error: Bam2Fastx Failed To Open Bam
tophat rna-seq bowtie mapping
updated 9.4 years ago by 20 • written 12.6 years ago by ▴ 960
25
votes
20
replies
20k
views
12 follow
Mapping Uniprot To Ensembl Genes
uniprot ensembl proteomics
updated 2.6 years ago by ▴ 280 • written 12.9 years ago by ▴ 960
4
votes
9
replies
12k
views
Adding Custom Bed And Bam Tracks To UCSC Browser By URL
ucsc genome browser bam bed
updated 10.4 years ago by ▴ 10 • written 12.2 years ago by ▴ 960
0
votes
1
reply
2.8k
views
Comment: Comment: interpreting minus strand reads in BAM?
updated 3.3 years ago by 45k • written 10.5 years ago by ▴ 960
0
votes
1
reply
2.8k
views
Comment: Comment: interpreting minus strand reads in BAM?
updated 3.3 years ago by 45k • written 10.5 years ago by ▴ 960
0
votes
5
replies
2.8k
views
interpreting minus strand reads in BAM?
next-gen alignment samtools bam RNA-Seq
updated 3.3 years ago by 45k • written 10.5 years ago by ▴ 960
9
votes
2
replies
4.5k
views
Telling Heterozygous Mutations From Tcga Maf Format?
tcga maf mutation genomics sequencing
updated 10.7 years ago by 20 • written 11.8 years ago by ▴ 960
0
votes
1
reply
11k
views
Comment: C: Gene set enrichment tool for RNA-Seq in Python?
11.0 years ago by user ▴ 960
21
votes
5
replies
14k
views
linking ensembl gene ID to GO term?
ucsc gene-ontology go gene-ids ensembl
updated 11.0 years ago by 11k • written 11.0 years ago by ▴ 960
6
votes
2
replies
10k
views
Obtaining Ucsc Tables Via Ftp And Converting Them To Proper Gff3 Via Genepredtogtf?
ucsc genes
updated 2.2 years ago by 45k • written 12.6 years ago by ▴ 960
3
votes
1
reply
2.4k
views
No PhyloP score for first stretch of chromosome?
alignment ucsc genome-browser phylop
updated 3.7 years ago by 45k • written 11.0 years ago by ▴ 960
0
votes
1
reply
2.6k
views
limit size of alignment generated by clustalw? Or related aligners?
alignment fasta phylogenomics comparative-genomics
11.1 years ago by user ▴ 960
7
votes
2
replies
7.3k
views
Detailed Explanation Of Ucsc Orientation / Coordinate Conversion For Minus Stranded Sequences?
strand dna alignment genome-browser
updated 11.1 years ago by 20 • written 11.3 years ago by ▴ 960
1
vote
1
reply
3.0k
views
Gene Expression Signatures For Basal Vs Mesenchymal Breast Tumors?
gene-expression clustering classification cancer genomics
updated 11.2 years ago by ★ 1.5k • written 11.2 years ago by ▴ 960
0
votes
1
reply
7.7k
views
Comment: C: Trouble Compiling C++ Code With Bamtools
11.2 years ago by user ▴ 960
54
votes
15
replies
32k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 6 months ago by ▴ 200 • written 11.8 years ago by ▴ 960
0
votes
1
reply
4.0k
views
Comprehensive Annotation Of Luminal/Basal For Breast Cancer Cell Line Microarray
microarray cancer genomics clustering
updated 11.2 years ago by 8.3k • written 11.2 years ago by ▴ 960
17
votes
6
replies
9.0k
views
Parameters That Determine Meme Speed And Homer Speed For Motif Discovery?
meme motif motif sequence
updated 11.3 years ago by 20 • written 12.2 years ago by ▴ 960
1
vote
2
replies
2.3k
views
Ucsc Track Friendly Format For Cds Sequences And Coordinates?
genome-browser fasta
updated 11.3 years ago by 105k • written 11.3 years ago by ▴ 960
0
votes
0
replies
7.3k
views
Comment: C: Detailed Explanation Of Ucsc Orientation / Coordinate Conversion For Minus Stran
11.3 years ago by user ▴ 960
6
votes
5
replies
3.8k
views
What Version Of Ensembl Is Ucsc Genome Browser Using?
ucsc genome-browser annotation ensembl
updated 11.4 years ago by 20 • written 11.8 years ago by ▴ 960
0
votes
0
replies
9.3k
views
Comment: C: How To Find Rna-Seq Data Of Published Papers?
11.8 years ago by user ▴ 960
18
votes
4
replies
9.3k
views
How To Find Rna-Seq Data Of Published Papers?
geo next-gen RNA-seq
updated 2.2 years ago by 45k • written 11.8 years ago by ▴ 960
0
votes
1
reply
16k
views
Comment: C: Differences Between Eisen Hierarchical Clustering In Bioconductor/R Versus Heatm
11.8 years ago by user ▴ 960
9
votes
3
replies
16k
views
Differences Between Eisen Hierarchical Clustering In Bioconductor/R Versus Heatmap.2?
clustering r bioconductor gene-expression
updated 2.2 years ago by 45k • written 11.8 years ago by ▴ 960
0
votes
1
reply
32k
views
Comment: C: Where To Download Pam50 Gene Set?
11.8 years ago by user ▴ 960
0
votes
1
reply
32k
views
Comment: C: Where To Download Pam50 Gene Set?
11.8 years ago by user ▴ 960
0
votes
0
replies
32k
views
Comment: C: Where To Download Pam50 Gene Set?
11.8 years ago by user ▴ 960
10
votes
2
replies
8.4k
views
How To Register A Tool With Galaxy?
galaxy pipeline
updated 2.2 years ago by 45k • written 11.8 years ago by ▴ 960
1
vote
1
reply
3.8k
views
Comment: C: What Version Of Ensembl Is Ucsc Genome Browser Using?
11.8 years ago by user ▴ 960
2
votes
3
replies
2.9k
views
Getting Ucsc Headers For Tables Through Ftp Or Via Sql?
ucsc genome-browser annotation genes
11.8 years ago by user ▴ 960
0
votes
1
reply
2.9k
views
Comment: C: Getting Ucsc Headers For Tables Through Ftp Or Via Sql?
11.8 years ago by user ▴ 960
1
vote
0
replies
4.0k
views
Computing Dinucleotide Frequencies / Markov Models And Scoring Sequences In Python?
hmm sequence motif python biopython
11.9 years ago by user ▴ 960
2
votes
4
replies
9.5k
views
Orientation Of Sequence On Minus Strand In Ucsc Genome Browser
ucsc genome-browser sequence strand strand
updated 12.0 years ago by ★ 2.0k • written 12.0 years ago by ▴ 960
0
votes
1
reply
9.5k
views
Comment: C: Orientation Of Sequence On Minus Strand In Ucsc Genome Browser
12.0 years ago by user ▴ 960
0
votes
0
replies
2.7k
views
Converting Multiple Global Alignment From Clustalw To Pwm?
alignment multiple-alignment sequence motif
12.1 years ago by user ▴ 960
0
votes
0
replies
5.8k
views
Comment: C: Sequence Logos With Weblogo Scale
12.1 years ago by user ▴ 960
9
votes
7
replies
5.8k
views
Sequence Logos With Weblogo Scale
sequence alignment motif motif
updated 12.1 years ago by 36k • written 12.1 years ago by ▴ 960
0
votes
0
replies
5.8k
views
Comment: C: Sequence Logos With Weblogo Scale
12.1 years ago by user ▴ 960
0
votes
1
reply
5.8k
views
Comment: C: Sequence Logos With Weblogo Scale
12.1 years ago by user ▴ 960
1
vote
2
replies
4.9k
views
Removing Pcr Duplicates From Bam Without Collapsing Sequences By Position?
bam samtools next-gen rna-seq pcr alignment
updated 12.1 years ago by ★ 5.3k • written 12.1 years ago by ▴ 960
0
votes
1
reply
15k
views
Comment: C: Plotting Read Densities And Gene Tracks In R?
12.2 years ago by user ▴ 960
10
votes
5
replies
15k
views
Plotting Read Densities And Gene Tracks In R?
gff genes rna-seq next-gen bam visualization r
updated 12.2 years ago by 27k • written 12.2 years ago by ▴ 960
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