ShanZhengYang's user avatar
ShanZhengYang's user avatar
ShanZhengYang's user avatar
ShanZhengYang
  • Member for 6 years, 7 months
  • Last seen more than 4 years ago
16 votes
3 answers
5k views

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

13 votes
3 answers
366 views

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

11 votes
3 answers
7k views

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

9 votes
2 answers
6k 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
3 answers
734 views

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

7 votes
5 answers
575 views

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

7 votes
3 answers
4k views

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

7 votes
2 answers
135 views

How to release an R package with several bed files?

7 votes
5 answers
979 views

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

7 votes
2 answers
3k views

Extracting the CIGAR string from a BAM via Python?

6 votes
3 answers
850 views

Generating the reconstructed alignment from BAM

6 votes
3 answers
11k views

How to concatenate "by chromosome"-VCFs?

6 votes
2 answers
307 views

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

6 votes
2 answers
432 views

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

5 votes
2 answers
707 views

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

4 votes
2 answers
704 views

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

4 votes
1 answer
358 views

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

4 votes
2 answers
272 views

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

4 votes
1 answer
4k views

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

3 votes
2 answers
516 views

Parse BAM by insertion size and get genomic coordinates

2 votes
1 answer
771 views

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

0 votes
2 answers
959 views

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