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747
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Comment: Comment: Computing pairwise AA global sequence alignment between all pairs in a vector of
8 months ago by rubic ▴ 270
0
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1
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747
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Comment: Comment: Computing pairwise AA global sequence alignment between all pairs in a vector of
8 months ago by rubic ▴ 270
2
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4
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747
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Computing pairwise AA global sequence alignment between all pairs in a vector of sequences
pairwiseAlignment
8 months ago by rubic ▴ 270
0
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0
replies
698
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Comment: Comment: Gene set enrichment analysis for genetic interactions
12 months ago by rubic ▴ 270
0
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0
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698
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Comment: Comment: Gene set enrichment analysis for genetic interactions
12 months ago by rubic ▴ 270
1
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3
replies
698
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Gene set enrichment analysis for genetic interactions
gsea genetic-interactions
12 months ago by rubic ▴ 270
1
vote
1
reply
746
views
Handling NA values in limma's voom design matrix
rna-seq voom design.matrix limma NA
updated 23 months ago by 82k • written 23 months ago by ▴ 270
0
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1
reply
425
views
Extract primary STAR mapped reads to specific chromosomes
samtools STAR
updated 2.2 years ago by ★ 1.5k • written 2.3 years ago by ▴ 270
1
vote
1
reply
613
views
Quantifying expression levels of IsoSeq reads with Kallisto
IsoSeq Kallisto expression
updated 2.3 years ago by ★ 5.9k • written 2.3 years ago by ▴ 270
0
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0
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1.0k
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Comment: Comment: Distinguishing between ambiguously mapped reads in a split bamToBed file
2.4 years ago by rubic ▴ 270
1
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2
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1.0k
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Distinguishing between ambiguously mapped reads in a split bamToBed file
reads RNA-Seq bam bamToBed split
2.4 years ago by rubic ▴ 270
2
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1
reply
512
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Extract the mapped portion of the read sequence
bam RNA-Seq cigar
updated 2.4 years ago by 82k • written 2.4 years ago by ▴ 270
2
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1
reply
573
views
Usage of bedTools
bedTools bamToBed
2.4 years ago by rubic ▴ 270
0
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0
replies
403
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Extract overlapping sequences from a bam file
bam RNA-Seq split splicing cigar
2.4 years ago by rubic ▴ 270
1
vote
1
reply
766
views
Downloading the IMGT/V-QUEST software
vquest software
updated 15 months ago by ▴ 990 • written 2.4 years ago by ▴ 270
1
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0
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500
views
Biostrings readDNAStringSet handling of N bases
Biostrings
2.6 years ago by rubic ▴ 270
0
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0
replies
864
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HLA haplotypes VCF
HLA Haplotype VCF
2.8 years ago by rubic ▴ 270
0
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1
reply
2.1k
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Comment: Comment: Fast parsing genbank files
3.1 years ago by rubic ▴ 270
0
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1
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2.1k
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Comment: Comment: Fast parsing genbank files
3.1 years ago by rubic ▴ 270
3
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5
replies
2.1k
views
Fast parsing genbank files
Genbank parsing R
updated 3.1 years ago by 100k • written 3.1 years ago by ▴ 270
0
votes
1
reply
977
views
Blast a CDD PSSM against a genome
pssm CDD blast
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 270
0
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1
reply
1.1k
views
Comment: Comment: Searching for conserved domains in a chromosome/scaffold
3.1 years ago by rubic ▴ 270
1
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3
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1.1k
views
Searching for conserved domains in a chromosome/scaffold
blast domain CDD PSSM rpsblast
updated 3.1 years ago by ★ 27k • written 3.1 years ago by ▴ 270
1
vote
1
reply
952
views
Getting all the genomic coordinates where RNA-seq reads are split within a given genomic interval in a bam file
RNA-Seq bam splicing cigar reads
updated 3.3 years ago by 161k • written 3.3 years ago by ▴ 270
2
votes
1
reply
1.2k
views
GET Ensembl xrefs for multiple queries
ensembl httr api
updated 3.7 years ago by ★ 2.4k • written 3.7 years ago by ▴ 270
1
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0
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4.7k
views
Answer: A: Create a UCSC chain file from a VCF
updated 4.4 years ago by 43k • written 10.0 years ago by ▴ 270
0
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1
reply
4.7k
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Comment: C: Create a UCSC chain file from a VCF
updated 4.4 years ago by 43k • written 10.0 years ago by ▴ 270
1
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0
replies
12k
views
Comment: C: Efficiently extract alignments with NH:i:1 field
updated 4.5 years ago by 43k • written 8.8 years ago by ▴ 270
0
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1
reply
1.5k
views
Comment: C: Get Ensembl mapping between the chromosome and scaffold names
4.9 years ago by rubic ▴ 270
0
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0
replies
1.5k
views
Comment: C: Get Ensembl mapping between the chromosome and scaffold names
4.9 years ago by rubic ▴ 270
3
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5
replies
1.5k
views
Get Ensembl mapping between the chromosome and scaffold names
ensembl Assembly scaffold chromosome
updated 4.9 years ago by ▴ 290 • written 4.9 years ago by ▴ 270
0
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0
replies
1.6k
views
Comment: C: AGP files in Ensembl
5.0 years ago by rubic ▴ 270
1
vote
4
replies
1.6k
views
AGP files in Ensembl
Assembly AGP ensembl
updated 5.0 years ago by 23k • written 5.0 years ago by ▴ 270
0
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1
reply
1.0k
views
Parse sim4 output alignment format
sim4 pairwise alignment parse
5.2 years ago by rubic ▴ 270
2
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2
replies
1.7k
views
Error while building picard tools from broadinstitute-picard-a4d54b4
picard broad
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 270
0
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1
reply
1.3k
views
Getting transcriptomic coordinates for CDS exons from a GTF
GTF BED
6.1 years ago by rubic ▴ 270
0
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0
replies
1.6k
views
Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
6.1 years ago by rubic ▴ 270
0
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1
reply
1.6k
views
Comment: C: Running salmon after subsetting the bam to transcripts annotated as protein codi
6.1 years ago by rubic ▴ 270
1
vote
4
replies
1.6k
views
Running salmon after subsetting the bam to transcripts annotated as protein coding in the GTF
salmon samtools GTF gencode
6.1 years ago by rubic ▴ 270
1
vote
1
reply
1.9k
views
Does samtools view -b -h <input.bam> -L <input.bed> keep the original header?
samtools header
updated 6.1 years ago by ★ 2.9k • written 6.1 years ago by ▴ 270
0
votes
1
reply
1.1k
views
Number of sequenced positions from a BAM file
bam samtools RNA-Seq
updated 7.0 years ago by 104k • written 7.0 years ago by ▴ 270
2
votes
1
reply
3.1k
views
Piping samtools merge to samtools calmd
samtools pipe
7.2 years ago by rubic ▴ 270
6
votes
7
replies
4.7k
views
Create a UCSC chain file from a VCF
genome vcf chain
updated 7.2 years ago by ★ 1.5k • written 10.0 years ago by ▴ 270
2
votes
1
reply
3.4k
views
Parsing BLAST pairwise output in R
R blast parse
7.3 years ago by rubic ▴ 270
0
votes
1
reply
1.7k
views
Pruning a reference phylogenetic tree according to input species
phylogenetics taxonomy
updated 7.3 years ago by ★ 3.0k • written 7.5 years ago by ▴ 270
9
votes
7
replies
6.9k
views
Count and location of strings in fastq file reads
RNA-Seq kmer suffix tree
updated 7.4 years ago by 11k • written 7.8 years ago by ▴ 270
0
votes
1
reply
1.6k
views
Finding clusters of interacting proteins in a protein-protein interaction graph
ppi graph protein-protein-interaction enrichment
updated 7.4 years ago by ▴ 650 • written 7.4 years ago by ▴ 270
6
votes
2
replies
4.0k
views
Piping a bam file to samtools calmd
samtools calmd pipe
updated 7.4 years ago by 7.4k • written 7.4 years ago by ▴ 270
2
votes
0
replies
2.3k
views
Producing transcriptomic bam with STAR with all sam attributes
RNA-Seq STAR
updated 7.4 years ago by 12k • written 7.4 years ago by ▴ 270
1
vote
1
reply
3.9k
views
Annotating gene clusters in a heatmap with GO enriched terms
RNA-Seq GO heatmap
updated 7.4 years ago by • 0 • written 7.4 years ago by ▴ 270
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