User ShanZhengYang

15 votes

3 answers

4k views

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

r bioconductor

asked Jan 22, 2018 at 17:01

13 votes

3 answers

348 views

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

asked May 20, 2017 at 21:49

11 votes

3 answers

6k views

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

r python fasta vcf samtools

asked Nov 12, 2017 at 10:27

8 votes

2 answers

4k views

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

vcf variant-calling maf

asked Jan 27, 2018 at 22:01

8 votes

4 answers

1k views

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

bam fasta vcf reference-genome variation

asked Aug 6, 2017 at 19:26

7 votes

5 answers

502 views

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

motifs software-recommendation

asked Jun 8, 2017 at 20:21

7 votes

3 answers

634 views

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

bam samtools sam

asked Aug 22, 2017 at 20:51

7 votes

3 answers

3k views

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

bam samtools reads

asked Oct 1, 2017 at 20:20

7 votes

2 answers

119 views

How to release an R package with several bed files?

r bed

asked Nov 3, 2017 at 0:33

7 votes

2 answers

2k views

Extracting the CIGAR string from a BAM via Python?

python bam pysam cigar

asked Mar 9, 2018 at 18:09

6 votes

2 answers

392 views

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

variation indel literature-search

asked Jun 19, 2017 at 20:49

6 votes

3 answers

605 views

Generating the reconstructed alignment from BAM

r python bam alignment sequence-alignment

asked Mar 1, 2018 at 4:07

6 votes

2 answers

258 views

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

rna-seq software-recommendation rna algorithms

asked Nov 23, 2017 at 21:21

6 votes

5 answers

795 views

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

human-genome genome reference-genome

asked Jun 24, 2017 at 23:33

5 votes

3 answers

8k views

How to concatenate "by chromosome"-VCFs?

vcf vcftools

asked Jan 14, 2018 at 21:38

5 votes

2 answers

576 views

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

python alignment biopython reference-genome

asked Sep 13, 2017 at 22:45

4 votes

2 answers

598 views

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

repeat centromere telomere

asked Sep 28, 2017 at 16:17

4 votes

2 answers

236 views

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

biopython bed structural-variation indel simulated-data

asked Jun 20, 2017 at 19:23

4 votes

1 answer

296 views

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

r bioconductor reference-genome snp biostrings

asked Aug 10, 2017 at 22:22

4 votes

1 answer

3k views

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

python vcf

asked Dec 15, 2017 at 19:19

3 votes

2 answers

397 views

Parse BAM by insertion size and get genomic coordinates

bam samtools

asked Feb 8, 2018 at 19:47

2 votes

1 answer

739 views

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

bam public-databases maf

asked Jan 26, 2018 at 16:55

0 votes

2 answers

654 views

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

bigwig validation

asked Feb 2, 2018 at 23:42

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23 Questions

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

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

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

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

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

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

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

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

How to release an R package with several bed files?

Extracting the CIGAR string from a BAM via Python?

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

Generating the reconstructed alignment from BAM

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

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

How to concatenate "by chromosome"-VCFs?

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

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

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

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

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

Parse BAM by insertion size and get genomic coordinates

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

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