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2
votes
2
replies
229
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Is refSeq table DNA or RNA coordinate?
RefSeq UCSC NCBI
updated 6 weeks ago by 142k • written 6 weeks ago by ▴ 170
11
votes
3
replies
827
views
is oxford nanopore technology data paired or single end sequencing?
oxford-nanopore DNA RNA
updated 3 months ago by 43k • written 3 months ago by ▴ 170
0
votes
0
replies
540
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Comment: Comment: should I use normalized counts or transformed of normalized counts for RNA-seq a
6 months ago by Alewa ▴ 170
1
vote
2
replies
540
views
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?
methylation DESeq RNA-Seq
6 months ago by Alewa ▴ 170
1
vote
0
replies
329
views
how to get genomic locations of Sequence patterns in R
R GenomicRanges Biostrings bioconductor
7 months ago by Alewa ▴ 170
1
vote
0
replies
583
views
Comment: Comment: bedtools intersect by position & stand not working even with common regions
7 months ago by Alewa ▴ 170
2
votes
2
replies
583
views
bedtools intersect by position & stand not working even with common regions
bedtools genomic intersect bedops intervals
7 months ago by Alewa ▴ 170
4
votes
3
replies
828
views
count number of GC for a given genomic ranges
bsgenome biostrings epigenetics
updated 9 months ago by 82k • written 9 months ago by ▴ 170
0
votes
1
reply
656
views
bioconductor caches fails to load/corrupted for annotation databases
TxDb.Hsapiens.UCSC.hg19.knownGene BiocFileCache AnnotationDbi R
updated 11 months ago by 43k • written 11 months ago by ▴ 170
1
vote
0
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411
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Answer: Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
11 months ago by Alewa ▴ 170
1
vote
1
reply
411
views
plyranges:: summarise() not recognizing previous summarized column (counts)
cpg R plyranges
11 months ago by Alewa ▴ 170
0
votes
0
replies
697
views
Comment: Comment: how to intersect multiple bed files and get results in uncollapsed genomic inter
11 months ago by Alewa ▴ 170
1
vote
2
replies
697
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools bedops
updated 10 months ago by 43k • written 11 months ago by ▴ 170
0
votes
1
reply
460
views
How to find complete overlaps between between multiple .bed files with bedtools
bedtools granges
updated 12 months ago by 161k • written 12 months ago by ▴ 170
0
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0
replies
1.1k
views
Comment: Comment: chromosome start & end for genes in biomart R not showing
16 months ago by Alewa ▴ 170
0
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0
replies
1.1k
views
Comment: Comment: chromosome start & end for genes in biomart R not showing
16 months ago by Alewa ▴ 170
3
votes
5
replies
1.1k
views
chromosome start & end for genes in biomart R not showing
ensembl bioconductor biomart
updated 16 months ago by 43k • written 16 months ago by ▴ 170
1
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0
replies
1.6k
views
Comment: Comment: where to find mouse genome GRCm38/mm10 for biomart R
16 months ago by Alewa ▴ 170
4
votes
2
replies
1.6k
views
where to find mouse genome GRCm38/mm10 for biomart R
ensembl bioconductor mouse biomart
16 months ago by Alewa ▴ 170
0
votes
1
reply
1.7k
views
Comment: Comment: gene symbol not showing for ensembl gene ids using biomart
16 months ago by Alewa ▴ 170
5
votes
5
replies
1.7k
views
gene symbol not showing for ensembl gene ids using biomart
ensembl biomart bioconductor refseq
updated 16 months ago by 43k • written 16 months ago by ▴ 170
0
votes
0
replies
583
views
Comment: Comment: How to insert quotes around description of format field in vcf header?
22 months ago by Alewa ▴ 170
2
votes
2
replies
583
views
How to insert quotes around description of format field in vcf header?
vcf bcftools
22 months ago by Alewa ▴ 170
0
votes
0
replies
709
views
Comment: Comment: How is contig length calculated ?
23 months ago by Alewa ▴ 170
3
votes
2
replies
709
views
How is contig length calculated ?
tuberculosis Contig assembly Genome Mycobacterium
23 months ago by Alewa ▴ 170
0
votes
1
reply
762
views
Comment: Comment: Why are number of CDS smaller than corresponding genes [M. tb]
24 months ago by Alewa ▴ 170
4
votes
3
replies
762
views
Why are number of CDS smaller than corresponding genes [M. tb]
NCBI entrez bash genes
updated 24 months ago by 21k • written 24 months ago by ▴ 170
0
votes
0
replies
527
views
Comment: Comment: [out of memory issue] NCBI Entrez protein seq download
24 months ago by Alewa ▴ 170
2
votes
2
replies
527
views
[out of memory issue] NCBI Entrez protein seq download
NCBI entrez bash protein
24 months ago by Alewa ▴ 170
10
votes
5
replies
4.9k
views
How to generate start & end coordinates for each chromosome of human ref genome in bed. format (0-based index)
bed bedtools bioconductor genome
updated 2.9 years ago by 14k • written 4.2 years ago by ▴ 170
0
votes
0
replies
1.8k
views
Comment: Comment: Segmentation fault in bcftools while changing the sample names
3.1 years ago by Alewa ▴ 170
0
votes
0
replies
720
views
How to covert VCF-like to ICGC-like vcf Format
conversion annotation
3.1 years ago by Alewa ▴ 170
0
votes
0
replies
4.4k
views
Comment: C: [GRanges] How to append query metadata to subjectHits
3.4 years ago by Alewa ▴ 170
4
votes
2
replies
4.4k
views
[GRanges] How to append query metadata to subjectHits
R granges bioconductor findOverlaps
updated 3.4 years ago by ★ 2.9k • written 3.4 years ago by ▴ 170
0
votes
1
reply
1.6k
views
Comment: A: Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinate
3.8 years ago by Alewa ▴ 170
0
votes
3
replies
1.6k
views
Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinates
Ensembl genome hg38 assembly liftover
3.8 years ago by Alewa ▴ 170
5
votes
0
replies
2.2k
views
Answer: A: what is the difference between calling variants with and without interval list?
3.8 years ago by Alewa ▴ 170
0
votes
0
replies
861
views
filtered and dropped vcfs empty when filtering 1000 gemomes variants with Annova
germline annovar 1000genomes annotation
3.8 years ago by Alewa ▴ 170
2
votes
0
replies
2.9k
views
Answer: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
3.9 years ago by Alewa ▴ 170
0
votes
1
reply
2.9k
views
Comment: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
3.9 years ago by Alewa ▴ 170
2
votes
4
replies
2.9k
views
[R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserved words. this is not the case
R GenomicRanges bioconductor
updated 3.9 years ago by 88k • written 3.9 years ago by ▴ 170
1
vote
0
replies
1.9k
views
Answer: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
3.9 years ago by Alewa ▴ 170
1
vote
5
replies
1.9k
views
Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped) ]
SNP bash vcf bcftools gatk
3.9 years ago by Alewa ▴ 170
0
votes
0
replies
1.7k
views
[R] subsetByOverlaps (Granges list and Granges object) not giving specific hits
R GenomicFeatures bioconductor
3.9 years ago by Alewa ▴ 170
0
votes
1
reply
1.9k
views
Comment: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.1 years ago by Alewa ▴ 170
0
votes
0
replies
1.9k
views
Comment: C: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.1 years ago by Alewa ▴ 170
0
votes
0
replies
1.6k
views
Comment: C: how to concetanate column values of a data frame and converting single letters o
4.1 years ago by Alewa ▴ 170
1
vote
0
replies
4.9k
views
Comment: C: How to generate start & end coordinates for each chromosome of human ref genome
4.2 years ago by Alewa ▴ 170
0
votes
0
replies
1.4k
views
Answer: A: Somatic mutations per gene
4.3 years ago by Alewa ▴ 170
0
votes
1
reply
2.0k
views
Comment: C: db-GaP / GTEx analysis on the cloud. Easiest way?
4.5 years ago by Alewa ▴ 170
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