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2
votes
2
replies
374
views
Is refSeq table DNA or RNA coordinate?
RefSeq UCSC NCBI
updated 7 months ago by 147k • written 7 months ago by ▴ 170
14
votes
3
replies
1.8k
views
is oxford nanopore technology data paired or single end sequencing?
oxford-nanopore DNA RNA
updated 9 months ago by 44k • written 9 months ago by ▴ 170
0
votes
0
replies
726
views
Comment: Comment: should I use normalized counts or transformed of normalized counts for RNA-seq a
13 months ago by Alewa ▴ 170
1
vote
2
replies
726
views
should I use normalized counts or transformed of normalized counts for RNA-seq association analysis?
methylation DESeq RNA-Seq
13 months ago by Alewa ▴ 170
1
vote
0
replies
423
views
how to get genomic locations of Sequence patterns in R
R GenomicRanges Biostrings bioconductor
13 months ago by Alewa ▴ 170
1
vote
0
replies
715
views
Comment: Comment: bedtools intersect by position & stand not working even with common regions
14 months ago by Alewa ▴ 170
2
votes
2
replies
715
views
bedtools intersect by position & stand not working even with common regions
bedtools genomic intersect bedops intervals
14 months ago by Alewa ▴ 170
4
votes
3
replies
1.1k
views
count number of GC for a given genomic ranges
bsgenome biostrings epigenetics
updated 15 months ago by 85k • written 15 months ago by ▴ 170
0
votes
1
reply
830
views
bioconductor caches fails to load/corrupted for annotation databases
TxDb.Hsapiens.UCSC.hg19.knownGene BiocFileCache AnnotationDbi R
updated 17 months ago by 44k • written 17 months ago by ▴ 170
1
vote
0
replies
504
views
Answer: Answer: plyranges:: summarise() not recognizing previous summarized column (counts)
17 months ago by Alewa ▴ 170
1
vote
1
reply
504
views
plyranges:: summarise() not recognizing previous summarized column (counts)
cpg R plyranges
17 months ago by Alewa ▴ 170
0
votes
0
replies
850
views
Comment: Comment: how to intersect multiple bed files and get results in uncollapsed genomic inter
18 months ago by Alewa ▴ 170
1
vote
2
replies
850
views
how to intersect multiple bed files and get results in uncollapsed genomic intervals
bedtools bedops
updated 17 months ago by 44k • written 18 months ago by ▴ 170
0
votes
1
reply
566
views
How to find complete overlaps between between multiple .bed files with bedtools
bedtools granges
updated 18 months ago by 164k • written 18 months ago by ▴ 170
0
votes
0
replies
1.3k
views
Comment: Comment: chromosome start & end for genes in biomart R not showing
22 months ago by Alewa ▴ 170
0
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0
replies
1.3k
views
Comment: Comment: chromosome start & end for genes in biomart R not showing
22 months ago by Alewa ▴ 170
3
votes
5
replies
1.3k
views
chromosome start & end for genes in biomart R not showing
ensembl bioconductor biomart
updated 22 months ago by 44k • written 22 months ago by ▴ 170
1
vote
0
replies
2.1k
views
Comment: Comment: where to find mouse genome GRCm38/mm10 for biomart R
22 months ago by Alewa ▴ 170
6
votes
2
replies
2.1k
views
where to find mouse genome GRCm38/mm10 for biomart R
ensembl bioconductor mouse biomart
22 months ago by Alewa ▴ 170
0
votes
1
reply
2.2k
views
Comment: Comment: gene symbol not showing for ensembl gene ids using biomart
23 months ago by Alewa ▴ 170
5
votes
5
replies
2.2k
views
gene symbol not showing for ensembl gene ids using biomart
ensembl biomart bioconductor refseq
updated 22 months ago by 44k • written 23 months ago by ▴ 170
0
votes
0
replies
697
views
Comment: Comment: How to insert quotes around description of format field in vcf header?
2.4 years ago by Alewa ▴ 170
2
votes
2
replies
697
views
How to insert quotes around description of format field in vcf header?
vcf bcftools
2.4 years ago by Alewa ▴ 170
0
votes
0
replies
853
views
Comment: Comment: How is contig length calculated ?
2.4 years ago by Alewa ▴ 170
3
votes
2
replies
853
views
How is contig length calculated ?
tuberculosis Contig assembly Genome Mycobacterium
2.4 years ago by Alewa ▴ 170
0
votes
1
reply
923
views
Comment: Comment: Why are number of CDS smaller than corresponding genes [M. tb]
2.5 years ago by Alewa ▴ 170
4
votes
3
replies
923
views
Why are number of CDS smaller than corresponding genes [M. tb]
NCBI entrez bash genes
updated 2.5 years ago by 21k • written 2.5 years ago by ▴ 170
0
votes
0
replies
636
views
Comment: Comment: [out of memory issue] NCBI Entrez protein seq download
2.5 years ago by Alewa ▴ 170
2
votes
2
replies
636
views
[out of memory issue] NCBI Entrez protein seq download
NCBI entrez bash protein
2.5 years ago by Alewa ▴ 170
10
votes
5
replies
5.6k
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 3.4 years ago by 14k • written 4.7 years ago by ▴ 170
0
votes
0
replies
2.0k
views
Comment: Comment: Segmentation fault in bcftools while changing the sample names
3.7 years ago by Alewa ▴ 170
0
votes
0
replies
810
views
How to covert VCF-like to ICGC-like vcf Format
conversion annotation
3.7 years ago by Alewa ▴ 170
0
votes
0
replies
5.1k
views
Comment: C: [GRanges] How to append query metadata to subjectHits
4.0 years ago by Alewa ▴ 170
4
votes
2
replies
5.1k
views
[GRanges] How to append query metadata to subjectHits
R granges bioconductor findOverlaps
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by ▴ 170
0
votes
1
reply
1.8k
views
Comment: A: Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinate
4.3 years ago by Alewa ▴ 170
0
votes
3
replies
1.8k
views
Convert list of ensembl Human genes -GRCh38.p13- from biomart to hg38 coordinates
Ensembl genome hg38 assembly liftover
4.3 years ago by Alewa ▴ 170
5
votes
0
replies
2.3k
views
Answer: A: what is the difference between calling variants with and without interval list?
4.3 years ago by Alewa ▴ 170
0
votes
0
replies
963
views
filtered and dropped vcfs empty when filtering 1000 gemomes variants with Annova
germline annovar 1000genomes annotation
4.3 years ago by Alewa ▴ 170
2
votes
0
replies
3.2k
views
Answer: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
4.4 years ago by Alewa ▴ 170
0
votes
1
reply
3.2k
views
Comment: C: [R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserv
4.4 years ago by Alewa ▴ 170
2
votes
4
replies
3.2k
views
[R] makeGRangesFromDataFrame errors that metadata columns (in dframe) has reserved words. this is not the case
R GenomicRanges bioconductor
updated 4.4 years ago by 88k • written 4.4 years ago by ▴ 170
1
vote
0
replies
2.1k
views
Answer: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.4 years ago by Alewa ▴ 170
1
vote
5
replies
2.1k
views
Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped) ]
SNP bash vcf bcftools gatk
4.4 years ago by Alewa ▴ 170
0
votes
0
replies
1.8k
views
[R] subsetByOverlaps (Granges list and Granges object) not giving specific hits
R GenomicFeatures bioconductor
4.4 years ago by Alewa ▴ 170
0
votes
1
reply
2.1k
views
Comment: A: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.6 years ago by Alewa ▴ 170
0
votes
0
replies
2.1k
views
Comment: C: Rename sample names in g.vcf files fails [Error Segmentation fault (core dumped)
4.6 years ago by Alewa ▴ 170
0
votes
0
replies
1.8k
views
Comment: C: how to concetanate column values of a data frame and converting single letters o
4.6 years ago by Alewa ▴ 170
1
vote
0
replies
5.6k
views
Comment: C: How to generate start & end coordinates for each chromosome of human ref genome
4.7 years ago by Alewa ▴ 170
0
votes
0
replies
1.5k
views
Answer: A: Somatic mutations per gene
4.8 years ago by Alewa ▴ 170
0
votes
1
reply
2.2k
views
Comment: C: db-GaP / GTEx analysis on the cloud. Easiest way?
5.0 years ago by Alewa ▴ 170
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