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6
votes
8
replies
5.0k
views
Modeling Chip-Seq Background Using Edger'S Glm Functionality?
chip-seq edger
updated 3.0 years ago by 82k • written 11.7 years ago by ★ 3.6k
11
votes
17
replies
6.5k
views
How Can I Save Bioperl Sequence Nested Features In Genbank Or Embl Format?
bioperl sequence data
updated 5.7 years ago by 43k • written 14.0 years ago by ★ 3.6k
48
votes
14
replies
22k
views
9 follow
What'S The Best Way To View And Explore A Large Gene Ontology Dag?
gene graphs visualization
updated 6.0 years ago by • 0 • written 13.9 years ago by ★ 3.6k
11
votes
11
replies
8.1k
views
Chipseq Background Subtraction For Count-Based Differential Binding Methods?
chip-seq edger
updated 7.2 years ago by 20 • written 11.7 years ago by ★ 3.6k
8
votes
4
replies
2.2k
views
Good Pdf Viewers For Plots With Thousands Of Points?
visualization
updated 2.3 years ago by 43k • written 10.4 years ago by ★ 3.6k
4
votes
5
replies
10k
views
Gene-Level Analysis Of Rna-Seq Matched Pairs Of Samples?
rna-seq
updated 7.5 years ago by 20 • written 11.8 years ago by ★ 3.6k
4
votes
7
replies
2.2k
views
Weird 1kb-periodic artifact in ChIP-Seq data (including input)
ChIP-Seq
7.5 years ago by Ryan Thompson ★ 3.6k
7
votes
6
replies
4.5k
views
Best aligner for reporting all exact matches of multi-mapping short reads?
miRNA alignment speed bowtie2
7.9 years ago by Ryan Thompson ★ 3.6k
2
votes
1
reply
2.8k
views
Is there a tool to convert soft clipping to hard clipping in bam files?
bam clipping
7.9 years ago by Ryan Thompson ★ 3.6k
11
votes
4
replies
3.8k
views
What Coordinate System Does Biomart Use?
biomart coordinates
updated 8.5 years ago by 20 • written 13.1 years ago by ★ 3.6k
4
votes
6
replies
7.2k
views
Cuffdiff Is Taking Forever. Can I Parallelize It?
cufflinks cuffdiff parallel
updated 8.7 years ago by 20 • written 12.7 years ago by ★ 3.6k
4
votes
3
replies
3.1k
views
How can I find the correct transformation for a continuous covariate in a gene expression linear model?
RNA-Seq linear-modeling covariates
8.9 years ago by Ryan Thompson ★ 3.6k
3
votes
4
replies
3.3k
views
Does It Makes Sense To Assemble All My Rna-Seq Samples As Though They Were One?
cufflinks transcriptome transcript assembly
updated 9.0 years ago by 20 • written 12.1 years ago by ★ 3.6k
18
votes
17
replies
24k
views
Processing Fastq Files In R/Bioconductor Without Reading Entire Files Into Memory?
r bioconductor fastq memory
9.1 years ago by Ryan Thompson ★ 3.6k
3
votes
4
replies
5.2k
views
Can I Pre-Build The Shared Transcriptome Index For A Series Of Tophat Runs?
tophat rna-seq
updated 9.4 years ago by ▴ 90 • written 11.9 years ago by ★ 3.6k
68
votes
23
replies
36k
views
16 follow
How Do I Do Simple Go Term Lookup Given A Gene (Or Mrna) Identifier?
gene annotation database
updated 3.1 years ago by 43k • written 14.0 years ago by ★ 3.6k
31
votes
2
replies
15k
views
Using A Variable As A Blocking Factor Vs Putting It As A Term In The Model Formula?
rna-seq limma edger deseq
updated 10.0 years ago by ▴ 110 • written 11.6 years ago by ★ 3.6k
2
votes
2
replies
5.6k
views
Where Do I Get A Gtf File With Proper Gene Ids For Read Counting?
rna-seq annotation
updated 10.2 years ago by 8.2k • written 11.5 years ago by ★ 3.6k
0
votes
2
replies
2.5k
views
What Is The Proper Way To Say "We Calculated Fdr Values From P-Values" In A Paper?
p-value
updated 10.3 years ago by 8.2k • written 10.3 years ago by ★ 3.6k
4
votes
6
replies
5.1k
views
Which Short Read Mappers Can Handle Overlapping Paired-End Reads?
paired short short aligner
updated 10.5 years ago by ★ 2.6k • written 13.2 years ago by ★ 3.6k
14
votes
4
replies
8.9k
views
K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
rna transcriptome next-gen sequencing assembly
updated 10.8 years ago by ▴ 410 • written 12.5 years ago by ★ 3.6k
13
votes
8
replies
11k
views
How Can I Accurately Identify Mirna Sequences From Small Rna Seq Results
mirna rna-seq alignment r
updated 10.8 years ago by 4.8k • written 10.8 years ago by ★ 3.6k
4
votes
2
replies
2.2k
views
Normalize A Single Array To An Already-Normalized Set Of Arrays?
microarray normalization
updated 11.0 years ago by 5.2k • written 11.0 years ago by ★ 3.6k
9
votes
5
replies
2.8k
views
Which Sequences Should I Include In A Whole Genome Alignment Of Primates?
alignment genome
updated 11.2 years ago by ▴ 530 • written 11.2 years ago by ★ 3.6k
6
votes
3
replies
4.4k
views
Is It Possible To Align A New Sequence With An Existing Maf Multiple Alignment?
alignment multiple-alignment
11.2 years ago by Ryan Thompson ★ 3.6k
14
votes
9
replies
6.4k
views
Why Does Chip-Seq Data Have Lots Of Reverse-Complement Pairs Of Reads?
chip-seq
updated 11.6 years ago by ★ 4.2k • written 12.2 years ago by ★ 3.6k
5
votes
3
replies
5.7k
views
Is There A Better Promoter Annotation Than Just Taking The 5-Prime Ends Of Ucsc Known Genes"?
chip-seq annotation
updated 11.6 years ago by 5.2k • written 11.6 years ago by ★ 3.6k
1
vote
2
replies
3.3k
views
How Do I Deal Programmatically With Retired Ensembl Ids?
ensembl
11.6 years ago by Ryan Thompson ★ 3.6k
2
votes
2
replies
3.7k
views
Differential Expression Analysis When Most Features Are Not Expected To Be Unchanged?
rna-seq
updated 11.7 years ago by 26k • written 11.7 years ago by ★ 3.6k
4
votes
5
replies
3.5k
views
Computing Relative Coordinates Of One Bioconductor Granges Object To Another?
bioconductor coordinates
updated 12.1 years ago by ★ 1.5k • written 12.1 years ago by ★ 3.6k
26
votes
9
replies
9.2k
views
Why Does Macs Use A Genome Size Of 2.7 Billion Instead Of 3 Billion For Human?
macs genome
updated 12.1 years ago by ★ 2.0k • written 12.1 years ago by ★ 3.6k
29
votes
6
replies
6.9k
views
6 follow
Is There Any Reason To Do De Novo Transcript Assembly If A Reference Is Available?
rna denovo trinity cufflinks
updated 12.1 years ago by ★ 1.5k • written 12.1 years ago by ★ 3.6k
7
votes
6
replies
5.5k
views
How Can I Identify Orthologous Contigs Between Two De Novo Transcriptome Assemblies?
transcriptome assembly denovo trinity orthologues
updated 12.4 years ago by ★ 2.5k • written 12.4 years ago by ★ 3.6k
22
votes
8
replies
8.6k
views
What Can I Do With Rna-Seq Samples With Major Genomic Contamination?
rna
updated 12.8 years ago by 54k • written 12.8 years ago by ★ 3.6k
13
votes
3
replies
5.4k
views
What Is The Typical Density Of Heterozygous Alleles In A Diploid Human Genome?
genomics haplotype
updated 12.8 years ago by 33k • written 13.2 years ago by ★ 3.6k
13
votes
7
replies
5.9k
views
6 follow
How Should I Compute Coverage When Some Reads Map To Multiple Locations?
sam bam coverage
updated 13.1 years ago by 22k • written 13.1 years ago by ★ 3.6k
8
votes
3
replies
4.3k
views
Does Liftover Have Single-Base Resolution?
liftover snp snp
updated 13.1 years ago by 5.0k • written 13.1 years ago by ★ 3.6k
18
votes
14
replies
12k
views
Semi-Global Alignment Tool?
alignment
updated 13.6 years ago by ▴ 410 • written 13.6 years ago by ★ 3.6k
8
votes
7
replies
3.6k
views
Biomart Yields Incomplete Results When Converting Refseq_Dna To Refseq_Peptide
biomart conversion
updated 13.6 years ago by • 0 • written 13.6 years ago by ★ 3.6k
1
vote
4
replies
3.0k
views
When Annotating Features On Sequences With Bioperl, What Is The Best Way To Pass The Annotated Sequences Between Scripts?
bioperl data perl sequence sequence
updated 14.0 years ago by ▴ 40 • written 14.0 years ago by ★ 3.6k
40 results • Page 1 of 1
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