Biostar Beta. Not for public use.
shawn.w.foley • 670
Status: New
Handle: @shawn.w.foley43234
Reputation: 670
Email: s*******@gsk.com
Joined: 13 months ago
Google Scholar: Shawn W Foley
Last seen: 17 months ago
Location: USA

Posts Awards
4
Votes
1
Reply
172
Views
A: issue with ifelse statement
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
214
Views
C: Removing adaptors from smallRNA seq data
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
151
Views
C: Label gene name using EnhancedVolcano
13 months ago
shawn.w.foley • 670
0
Votes
0
Replies
188
Views
C: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
13 months ago
shawn.w.foley • 670
3
Votes
1
Reply
188
Views
C: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
200
Views
C: any idea about histogram(graphic) clustering?
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
189
Views
C: Can I convert from PSI to RPKM?
13 months ago
shawn.w.foley • 670
2
Votes
2
Replies
189
Views
A: Can I convert from PSI to RPKM?
13 months ago
shawn.w.foley • 670
0
Votes
0
Replies
123
Views
C: gcRMA normalize and run differential expression for signal intensity data withou
13 months ago
shawn.w.foley • 670
0
Votes
0
Replies
174
Views
C: bioinformatics tools to connect modifications on RNA to its structure
13 months ago
shawn.w.foley • 670
1
Vote
2
Replies
123
Views
gcRMA normalize and run differential expression for signal intensity data without CEL files
microarray limma gcrma illumina
13 months ago
shawn.w.foley • 670 • updated 13 months ago
Kevin Blighe 43k
0
Votes
0
Replies
174
Views
C: bioinformatics tools to connect modifications on RNA to its structure
13 months ago
shawn.w.foley • 670
3
Votes
1
Reply
151
Views
A: Extract and retain only chromosome info in GWAS sumstats file
13 months ago
shawn.w.foley • 670
0
Votes
0
Replies
101
Views
A: Can detection of SNP from DNA (Intronic part) and mRNA (Exonic Part) make some
13 months ago
shawn.w.foley • 670
1
Vote
1
Reply
135
Views
A: How to group gene dataset and run t.test for each row for every gene in R?
13 months ago
shawn.w.foley • 670
2
Votes
2
Replies
1.1k
Views
ChIP-seq differential binding with multiple replicates using MACS2 bdgdiff.
ChIP-Seq MACS2 bdgdiff
2.3 years ago
shawn.w.foley • 670 • updated 13 months ago
ATpoint 17k
0
Votes
1
Reply
151
Views
C: CCLE miRNA expression data
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
151
Views
A: CCLE miRNA expression data
13 months ago
shawn.w.foley • 670
0
Votes
0
Replies
198
Views
C: Should I keep all HTSeq table informations for edgeR analysis?
13 months ago
shawn.w.foley • 670
0
Votes
1
Reply
198
Views
A: Should I keep all HTSeq table informations for edgeR analysis?
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
334
Views
C: upSet R plot for variant calling
14 months ago
shawn.w.foley • 670
0
Votes
0
Replies
158
Views
C: Tool to perform GSEA on mapped genes
14 months ago
shawn.w.foley • 670
0
Votes
0
Replies
146
Views
A: Variants in Exon or Intron
14 months ago
shawn.w.foley • 670
1
Vote
0
Replies
158
Views
A: Tool to perform GSEA on mapped genes
14 months ago
shawn.w.foley • 670
0
Votes
0
Replies
179
Views
A: Estimate percentage of alternative splicing
14 months ago
shawn.w.foley • 670
1
Vote
0
Replies
173
Views
C: Including bioinformatics into an agriculture/horticulture dissertation project
14 months ago
shawn.w.foley • 670
1
Vote
1
Reply
173
Views
C: Including bioinformatics into an agriculture/horticulture dissertation project
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
271
Views
C: Question about differentially expressed genes selection for low sample size data
14 months ago
shawn.w.foley • 670
2
Votes
1
Reply
271
Views
C: Question about differentially expressed genes selection for low sample size data
14 months ago
shawn.w.foley • 670
3
Votes
2
Replies
271
Views
A: Question about differentially expressed genes selection for low sample size data
14 months ago
shawn.w.foley • 670
2
Votes
1
Reply
201
Views
Mutect2 "somatic" variants with resistant tissue culture lines
mutect2 wes variants genotyping GATK
15 months ago
shawn.w.foley • 670 • updated 14 months ago
Biostar 20
4
Votes
1
Reply
172
Views
A: Trouble manipulating dataset
14 months ago
shawn.w.foley • 670
0
Votes
0
Replies
215
Views
C: Something strange in RNA-seq raw reads, It is contamination or not?
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
215
Views
A: Something strange in RNA-seq raw reads, It is contamination or not?
14 months ago
shawn.w.foley • 670
0
Votes
0
Replies
1.3k
Views
C: Is it possible to convert .CHP files to .CEL?
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
205
Views
C: Fold change cut off enrichment analysis
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
205
Views
A: Fold change cut off enrichment analysis
14 months ago
shawn.w.foley • 670
1
Vote
0
Replies
269
Views
C: Multiple testing correction issue
14 months ago
shawn.w.foley • 670
0
Votes
1
Reply
269
Views
A: Multiple testing correction issue
14 months ago
shawn.w.foley • 670
1
Vote
1
Reply
223
Views
C: RNA Seq analysis of rice samples
14 months ago
shawn.w.foley • 670
1
Vote
0
Replies
183
Views
A: RNA-Seq Analysis with DEXSeq
14 months ago
shawn.w.foley • 670
1
Vote
0
Replies
207
Views
C: which statistical test use for differential expression with qPCR
14 months ago
shawn.w.foley • 670
3
Votes
0
Replies
192
Views
A: RIP-seq identifing reverse complement reads between smallRNA and targeted mRNA
14 months ago
shawn.w.foley • 670
1
Vote
1
Reply
192
Views
C: RIP-seq identifing reverse complement reads between smallRNA and targeted mRNA
14 months ago
shawn.w.foley • 670
1
Vote
1
Reply
192
Views
C: RIP-seq identifing reverse complement reads between smallRNA and targeted mRNA
14 months ago
shawn.w.foley • 670
2
Votes
1
Reply
1.6k
Views
C: Middle author, but not first author projects. How would you approach this?
15 months ago
shawn.w.foley • 670
4
Votes
1
Reply
1.6k
Views
C: Middle author, but not first author projects. How would you approach this?
15 months ago
shawn.w.foley • 670
0
Votes
0
Replies
243
Views
A: Statistics on differentially expressed genes
15 months ago
shawn.w.foley • 670
2
Votes
0
Replies
190
Views
A: Writing scripts for a single vs all chromosomes
16 months ago
shawn.w.foley • 670
2
Votes
1
Reply
312
Views
C: Post PCA analysis
16 months ago
shawn.w.foley • 670
0
Votes
0
Replies
285
Views
C: CLIP-seq peak analysis
16 months ago
shawn.w.foley • 670
0
Votes
1
Reply
285
Views
C: CLIP-seq peak analysis
16 months ago
shawn.w.foley • 670
1
Vote
1
Reply
210
Views
C: Differential gene expression DESeq2
16 months ago
shawn.w.foley • 670
0
Votes
1
Reply
285
Views
C: CLIP-seq peak analysis
16 months ago
shawn.w.foley • 670
0
Votes
1
Reply
326
Views
C: Some problems with DEXSEQ analyse
16 months ago
shawn.w.foley • 670
0
Votes
0
Replies
323
Views
A: Transcription factor binding sites using ATAC-seq peaks
16 months ago
shawn.w.foley • 670
1
Vote
1
Reply
285
Views
A: CLIP-seq peak analysis
16 months ago
shawn.w.foley • 670
2
Votes
1
Reply
240
Views
C: Interpreting DEseq2 results
16 months ago
shawn.w.foley • 670
1
Vote
0
Replies
261
Views
C: Too low FPKM values from StringTie
16 months ago
shawn.w.foley • 670
1
Vote
1
Reply
261
Views
C: Too low FPKM values from StringTie
17 months ago
shawn.w.foley • 670
1
Vote
1
Reply
261
Views
C: Too low FPKM values from StringTie
17 months ago
shawn.w.foley • 670
0
Votes
0
Replies
212
Views
C: Unequally pooling libraries for RNAseq?
17 months ago
shawn.w.foley • 670
0
Votes
1
Reply
212
Views
A: Unequally pooling libraries for RNAseq?
17 months ago
shawn.w.foley • 670
0
Votes
1
Reply
242
Views
A: Get -400bp to +50bp sequence of gene from gff3 file
17 months ago
shawn.w.foley • 670
0
Votes
1
Reply
262
Views
C: How to identify translocation events within cell lines
17 months ago
shawn.w.foley • 670
0
Votes
1
Reply
262
Views
C: How to identify translocation events within cell lines
17 months ago
shawn.w.foley • 670
2
Votes
7
Replies
262
Views
How to identify translocation events within cell lines
translocation whole genome seq panel
17 months ago
shawn.w.foley • 670 • updated 17 months ago
Vitis ♦ 2.1k
0
Votes
0
Replies
262
Views
C: How to identify translocation events within cell lines
17 months ago
shawn.w.foley • 670
0
Votes
1
Reply
387
Views
C: After sorting bam file not able to index ?
18 months ago
shawn.w.foley • 670
0
Votes
0
Replies
206
Views
A: Finding deferentially active regions with DESeq2
18 months ago
shawn.w.foley • 670
0
Votes
0
Replies
251
Views
C: Filtering fastq vs BAM for fragment size range
18 months ago
shawn.w.foley • 670
1
Vote
0
Replies
351
Views
A: Venn diagram generation criteria from RNAseq data
19 months ago
shawn.w.foley • 670
0
Votes
1
Reply
410
Views
C: miRNA mRNA interaction studies
19 months ago
shawn.w.foley • 670
0
Votes
1
Reply
259
Views
C: General Question to shRNA-Seq analysis
20 months ago
shawn.w.foley • 670
0
Votes
2
Replies
280
Views
C: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
20 months ago
shawn.w.foley • 670
2
Votes
1
Reply
280
Views
A: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
20 months ago
shawn.w.foley • 670
0
Votes
1
Reply
280
Views
C: Extract rows from file two having the 4th column ( which contain /1 /2 signs ) i
20 months ago
shawn.w.foley • 670
2
Votes
2
Replies
816
Views
A: GSEA, input metrics
22 months ago
shawn.w.foley • 670
4
Votes
3
Replies
1.7k
Views
How do you compare GSEA results between treatments?
GSEA microarray
2.6 years ago
shawn.w.foley • 670 • updated 2.3 years ago
a_liberzon • 0
0
Votes
1
Reply
2.3k
Views
C: Analyzing RNA-seq without replicates
2.4 years ago
shawn.w.foley • 670
11
Votes
6
Replies
2.3k
Views
Analyzing RNA-seq without replicates
RNA-seq cufflinks DESeq2 isoem2 isode2
2.4 years ago
shawn.w.foley • 670 • updated 2.4 years ago
i.sudbery 4.7k
1
Vote
1
Reply
554
Views
C: How to find the gene structure of a gene?
2.5 years ago
shawn.w.foley • 670
1
Vote
1
Reply
13k
Views
C: R DESeq: What exactly is Variance Stabilizating Transformation?
2.5 years ago
shawn.w.foley • 670
0
Votes
0
Replies
816
Views
A: How do strand specific sequencing protocols work?
2.5 years ago
shawn.w.foley • 670
3
Votes
1
Reply
1.0k
Views
A: Replicates for RNA-seq from 1 cell lines undergoing different treatments
2.5 years ago
shawn.w.foley • 670
1
Vote
1
Reply
499
Views
How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or crlmm?
SNP bioconductor oligos crlmm
2.6 years ago
shawn.w.foley • 670
1
Vote
0
Replies
499
Views
A: How do I extract normalized signal values for Affy SNP 6.0 chip using oligo or c
2.6 years ago
shawn.w.foley • 670
0
Votes
0
Replies
601
Views
C: When performing Fisher's exact test, should I consider all annotated or all dete
2.6 years ago
shawn.w.foley • 670
3
Votes
2
Replies
601
Views
When performing Fisher's exact test, should I consider all annotated or all detected transcripts?
RNA-Seq fisher's test expression statistics
2.6 years ago
shawn.w.foley • 670 • updated 2.6 years ago
Hussain Ather • 920
Powered by the version 2.1