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ShanZhengYang
  • Member for 5 years
  • Last seen more than 2 years ago
15 votes
3 answers
4k views

R package development: How does one automatically install Bioconductor packages upon package installation?

13 votes
3 answers
348 views

Given a VCF of a human genome, how do I assess the quality against known SNVs?

11 votes
3 answers
6k views

Converting a VCF into a FASTA given a reference with Python, R

8 votes
2 answers
4k views

Tools to do VCF to MAF and MAF to VCF conversion?

8 votes
4 answers
1k views

How to manipulate a reference FASTA or bam to include variants from a VCF?

7 votes
5 answers
502 views

What motif finding software is available for multiple sequences ~10Kb?

7 votes
3 answers
634 views

Is there a way to retrieve several SAM fields faster than `samtools view | cut -f`?

7 votes
3 answers
3k views

How to check whether all BAM read contain defined read groups?

7 votes
2 answers
119 views

How to release an R package with several bed files?

7 votes
2 answers
2k views

Extracting the CIGAR string from a BAM via Python?

6 votes
2 answers
392 views

What is the distribution of indel sizes in a healthy human genome? of insertion:deletion ratios?

6 votes
3 answers
605 views

Generating the reconstructed alignment from BAM

6 votes
2 answers
258 views

Estimate the length of poly-A tails from randomly-primed RNAseq data

6 votes
5 answers
795 views

What is the standard way to work with a diploid reference genome? Complementary strands?

5 votes
3 answers
8k views

How to concatenate "by chromosome"-VCFs?

5 votes
2 answers
576 views

Is it possible to do alignment within Python? Check variants against reference?

4 votes
2 answers
598 views

How are centromeric/telomeric regions categorized in RepeatMasker? "Other" category?

4 votes
2 answers
236 views

After artificially creating events in a FASTA file, how do I keep track of the old coordinates?

4 votes
1 answer
296 views

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

4 votes
1 answer
3k views

Using Python, how to convert a pandas DataFrame into a VCF?

3 votes
2 answers
397 views

Parse BAM by insertion size and get genomic coordinates

2 votes
1 answer
739 views

Downloading an open-source MAF with tumor and normal BAMs?

0 votes
2 answers
654 views

Is there a standard method to validate whether a bigWig file is correct?