User: Ying W

gravatar for Ying W
Ying W3.9k
Reputation:
3,900
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Location:
South San Francisco, CA
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Last seen:
1 month, 1 week ago
Joined:
8 years, 5 months ago
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d*******@gmail.com

Bioinformatician working in biotech industry. Background is in computer science and genetics, did a PhD focusing to learn more about epigenetics and biostats. I've been working with sequencing data for quite a few years now, first on flies, then plants, and now with humans.

Posts by Ying W

<prev • 328 results • page 1 of 33 • next >
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Answer: A: What is differences and similarites between NCI60, CCLE, CMAP?
... - [NCI60](https://dtp.cancer.gov/discovery_development/nci-60/) contains data (growth inhibition / cell death) of 60 different cancer cell lines when exposed to many different types of compounds - [CCLE](https://portals.broadinstitute.org/ccle/home) contains data (RNA expression / DNA copy number ch ...
written 2.4 years ago by Ying W3.9k
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Job: R&D Scientist, Computational Biology - Agilent Technologies, Santa Clara, CA
... **Description**: Agilent Research Laboratories, which strives to power the growth of Agilent Technologies through breakthrough science and technology is seeking an enthusiastic, experienced and skilled computational biologist to work as part of innovative multidisciplinary team developing next gen ...
cloud job big data machine learning written 2.6 years ago by Ying W3.9k
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Comment: C: Batch correction for TCGA 450K data
... I think you need to correct for batches, have a look [here](http://bioinformatics.mdanderson.org/main/TCGABatchEffects:Overview) ...
written 3.0 years ago by Ying W3.9k
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Comment: C: RUVseq to correct for unwanted variance, interpreting p-value distribution
... you probably want to recreate the right plot in your first image also colored so that replicates are the same color. yea the p-value distribution looks weird in the last image. I would either not pool the other two when doing the comparison (so its always a 1 species vs another species comparison) ...
written 3.2 years ago by Ying W3.9k
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Answer: A: step by step mass spectrometry proteomics
... have a look here: https://www.bioconductor.org/packages/release/bioc/vignettes/RMassBank/inst/doc/RMassBank.pdf ...
written 3.2 years ago by Ying W3.9k
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Answer: A: Alternative for BGI WEGO
... you could try using DAVID but i am not too sure how common web based GO enrichment tools are nowadays. There was a post made a couple years ago but some of those links are dead: https://www.biostars.org/p/4302/ Gene Ontology website used to curate a list of tools but they removed it after warning t ...
written 3.2 years ago by Ying W3.9k
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Comment: C: RUVseq to correct for unwanted variance, interpreting p-value distribution
... have you looked at batch effects before using RUVseq? Is it proper to assume in your experimental setup that the 5000 transcripts would be non-DE? You can upload images to something like [imgur](http://imgur.com/) to show them in your question. ...
written 3.2 years ago by Ying W3.9k
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Answer: A: pipeline of analyses to identify functional loops of chromosomes
... The methods of this recent paper have a lot of manual transformations required. Pipelines are usually more common when a method becomes more established. My guess is that not that much high quality Hi-C data has been generated by enough different labs that everyone just does their own thing. ...
written 3.3 years ago by Ying W3.9k
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Answer: A: ENCODE DNase Hypersensitivity narrowPeak scores
... I'm pretty sure they are using hotspot not i-max. The word document on that page talks a bit about its scoring metric. ...
written 3.3 years ago by Ying W3.9k
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Answer: A: rsubread: featureCounts, extending ChIP-seq reads, counting the fragments
... > I want to count features falling in a specific genomic location using featureCounts from rsubreads. The point of read extension is to infer fragment size which is important when counting (esp for sharp peaks). > Does featureCount take into consideration the strand of the read when extendin ...
written 3.4 years ago by Ying W3.9k

Latest awards to Ying W

Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Predict Tfbs/Crms For A Species With No Chip-Seq Using Chip-Seq Data In Other Sp
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: What statistical test does DESeq use?
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Sliding Window for CNV Analysis
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Best Way To Preprocess Barcoded Illumina Paired-End Data
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: What Are The Best Bioinformatics Course Materials And Videos (Available Online)?
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Piping With Samtools, Bwa And Bedtools
Popular Question 2.2 years ago, created a question with more than 1,000 views. For R&D Scientist, Computational Biology - Agilent Technologies, Santa Clara, CA
Scholar 2.2 years ago, created an answer that has been accepted. For A: How can I programmatically download the GEO DataSets of a given accession?
Great Question 2.2 years ago, created a question with more than 5,000 views. For Best Way To Preprocess Barcoded Illumina Paired-End Data
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Comparing two ChIP-seq libraries
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: What Control For Chip-Seq: Input, Igg Or Untagged Strain?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How can I programmatically download the GEO DataSets of a given accession?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: What is the difference between fine-mapping and targeted sequencing?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Run multiple fastq.gz files with FastQC and yield single report?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Difference Between Picards Mergebamalignment And Mergesamfiles
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Seqlogo and Homer
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Best Practice Approach In R To Processing Illumina Microarrays For Rna Profilin
Student 2.2 years ago, asked a question with at least 3 up-votes. For Best Way To Preprocess Barcoded Illumina Paired-End Data
Student 2.2 years ago, asked a question with at least 3 up-votes. For Quantification And Comparison Of Chip-Seq Peaks
Scholar 2.2 years ago, created an answer that has been accepted. For A: What is the difference between fine-mapping and targeted sequencing?
Great Question 2.3 years ago, created a question with more than 5,000 views. For Best Way To Preprocess Barcoded Illumina Paired-End Data
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Bioinformatics courses, workshops or training.
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: How Do I Get A Gff Files Or Make My Own For A Bacteriophage?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For What Is The Best Way To Run Bedtools In Parallel With Blocking
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Chip-Seq Remove Centromeres

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