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Showing :
questions
1
vote
3
replies
1.5k
views
R design on 2-way interaction not displaying all options
modeling
design
limma
deseq
edger
updated 7 weeks ago by
mflab
• 0 • written 4.4 years ago by
fr
▴ 220
0
votes
2
replies
828
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 19 months ago by
ATpoint
86k • written 19 months ago by
fr
▴ 220
1
vote
0
replies
338
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
19 months ago by
fr
▴ 220
0
votes
0
replies
406
views
Positive TPM in genes with 0 counts from StringTie?
RNAseq
stringtie
24 months ago by
fr
▴ 220
0
votes
2
replies
1.3k
views
Retrieving and interpreting specific contrast results from an interaction experiment in DESeq2
deseq2
3.2 years ago by
fr
▴ 220
4
votes
4
replies
2.2k
views
Single-stranded RNA-seq: strandedness of samples
rnaseq
3.5 years ago by
fr
▴ 220
0
votes
0
replies
847
views
limma: extracting coefficients and design matrix?
limma
glm
updated 3.7 years ago by
cpad0112
21k • written 3.7 years ago by
fr
▴ 220
1
vote
3
replies
2.1k
views
limma: extracting coefficients for complex models
limma
r
3.7 years ago by
fr
▴ 220
0
votes
1
reply
1.7k
views
Benchmarking DESeq / EdgeR / LIMMA vs Lasso vs RF
deseq
edger
limma
lasso
RF
updated 4.1 years ago by
Biostar
20 • written 4.3 years ago by
fr
▴ 220
0
votes
2
replies
1.1k
views
Limma contrasts matrix drops columns and considers them as reference column
limma
design
updated 4.3 years ago by
Luiz
▴ 30 • written 4.3 years ago by
fr
▴ 220
3
votes
4
replies
1.3k
views
Limma contrasts and design: should it be split based on time points?
limma
design
4.3 years ago by
fr
▴ 220
4
votes
4
replies
2.9k
views
Computing significance of overlap between two gene lists in Python
python
hypergeometric
fishers
updated 4.6 years ago by
Biostar
20 • written 4.8 years ago by
fr
▴ 220
1
vote
3
replies
2.4k
views
RNAseq: should I trim both 3' and 5'?
RNA-Seq
updated 4.7 years ago by
swbarnes2
14k • written 4.7 years ago by
fr
▴ 220
2
votes
1
reply
1.4k
views
RNAseq: differences when shifting from 100bp to 150bp?
RNA-Seq
4.8 years ago by
fr
▴ 220
2
votes
0
replies
2.6k
views
Homer's findPeaks: normalized Tag counts, Peak Score, and RPKMs
ChIP-Seq
HOMER
atac-seq
5.0 years ago by
fr
▴ 220
0
votes
1
reply
1.4k
views
Strange output from Homer findPeaks
homer
atac-seq
updated 19 months ago by
Ram
44k • written 5.1 years ago by
fr
▴ 220
0
votes
0
replies
777
views
meaning of "Total subpeaks" in Homer's mergePeaks?
homer
ChIP-Seq
atac-seq
5.1 years ago by
fr
▴ 220
4
votes
2
replies
852
views
How to export more than 1000 entries in IPA
ipa
ingenuity pathway analysis
updated 5.1 years ago by
Biostar
20 • written 5.2 years ago by
fr
▴ 220
4
votes
9
replies
3.5k
views
How to view bigwig files in UCSC with windowed coverage?
ucsc
atac-seq
ChIP-Seq
updated 19 months ago by
Ram
44k • written 5.1 years ago by
fr
▴ 220
2
votes
1
reply
1.7k
views
Visualizing bigwig tracks
ChIP-Seq
RNA-Seq
updated 5.2 years ago by
colin.kern
★ 1.1k • written 5.2 years ago by
fr
▴ 220
3
votes
2
replies
1.6k
views
Homer annotatePeaks on genomic regions
homer
ChIP-Seq
annotatepeaks
updated 5.6 years ago by
bruss
▴ 30 • written 5.6 years ago by
fr
▴ 220
7
votes
3
replies
3.3k
views
How to bin my count data for the entire genome?
ChIP-Seq
next-gen
sequencing
genome
homer
updated 5.6 years ago by
Prakash
★ 2.2k • written 5.6 years ago by
fr
▴ 220
7
votes
9
replies
2.9k
views
Combine .bed files and keep columns / headers
bedtools
bedops
bedmap
updated 5.6 years ago by
ATpoint
86k • written 5.6 years ago by
fr
▴ 220
2
votes
1
reply
1.2k
views
Question about Bedtools intersect: allows for multiple matches?
bedtools
pybedtools
updated 5.7 years ago by
jared.andrews07
★ 18k • written 5.7 years ago by
fr
▴ 220
0
votes
0
replies
2.5k
views
pyBedTools.BedTools.intersect() not working on dataframe
bedtools
pybedtools
5.7 years ago by
fr
▴ 220
4
votes
5
replies
3.0k
views
Edit score column in bed file
bed
bedtools
updated 5.8 years ago by
Alex Reynolds
36k • written 5.8 years ago by
fr
▴ 220
2
votes
1
reply
4.4k
views
Homer not finding any genomes?
homer
hic
ChIP-Seq
5.9 years ago by
fr
▴ 220
2
votes
1
reply
4.5k
views
Enrichr : how to provide background as gene symbols or int ?
gene
RNA-Seq
microarray
gsea
5.9 years ago by
fr
▴ 220
4
votes
9
replies
2.1k
views
Genome-wide CRISPR/Cas9 and gene expression?
crispr
cas9
microarray
gene expression
updated 6.6 years ago by
GouthamAtla
12k • written 6.8 years ago by
fr
▴ 220
1
vote
3
replies
2.7k
views
Where to find CCLE metadata?
ccle
RNA-Seq
updated 6.7 years ago by
Biostar
20 • written 6.7 years ago by
fr
▴ 220
3
votes
14
replies
8.1k
views
RNA-seq data from CCLE - where are the details?
ccle
RNA-Seq
gene
updated 6.7 years ago by
Kevin Blighe
88k • written 6.7 years ago by
fr
▴ 220
0
votes
0
replies
1.2k
views
Error in PIANO
ChIP-Seq
R
PIANO
7.1 years ago by
fr
▴ 220
0
votes
1
reply
2.0k
views
Accessing legacy data in GDC
rna-seq
R
tcgabiolinks
updated 7.2 years ago by
Kevin Blighe
88k • written 7.6 years ago by
fr
▴ 220
0
votes
2
replies
1.7k
views
ID mapping: from Rat codelink to Entrez
ChIP-Seq
7.2 years ago by
fr
▴ 220
4
votes
5
replies
2.9k
views
Drug database for cell line experiments with before vs after treatment responses
cmap
RNA-Seq
ChIP-Seq
updated 7.2 years ago by
svlachavas
▴ 790 • written 7.2 years ago by
fr
▴ 220
5
votes
3
replies
2.9k
views
Correlating gene expression with qualitative variables
RNA-Seq
R
correlation
updated 7.6 years ago by
Nicolas Rosewick
11k • written 7.6 years ago by
fr
▴ 220
0
votes
1
reply
2.6k
views
R: Inconsistency between data from TCGAbiolinks and GDC (does TCGAbiolinks retrieve Legacy data by default?)
r
genome
rna-seq
8.0 years ago by
fr
▴ 220
5
votes
2
replies
4.2k
views
Is it possible to download cancer, normal, and matched tissue data from GDC? From same patient samples? How?
gdc
8.2 years ago by
fr
▴ 220
3
votes
6
replies
1.8k
views
Gene Ontology process to Ensembl (in Perl)?
gene ontology
ensembl
updated 8.3 years ago by
Ron
★ 1.2k • written 8.3 years ago by
fr
▴ 220
9
votes
23
replies
8.8k
views
How to retrieve gene sequences and their products from NCBI's FTP?
genome
gene
updated 3.0 years ago by
Ram
44k • written 10.3 years ago by
fr
▴ 220
0
votes
2
replies
3.1k
views
How to process reverse sequences?
genome
sequence
updated 2.2 years ago by
Ram
44k • written 9.5 years ago by
fr
▴ 220
0
votes
0
replies
1.7k
views
Getting intergenic sequences using BioPerl?
perl
genome
sequence
updated 2.5 years ago by
Ram
44k • written 9.5 years ago by
fr
▴ 220
3
votes
2
replies
2.2k
views
Tips to download pathway information from anywhere (but KEGG)?
pathway
updated 2.6 years ago by
Ram
44k • written 9.8 years ago by
fr
▴ 220
2
votes
3
replies
2.8k
views
Any tools for predicting protein solvent exposure/accessibility?
sequence
structure
protein structure
updated 2.7 years ago by
Ram
44k • written 9.9 years ago by
fr
▴ 220
4
votes
3
replies
2.1k
views
How to skip a genebank file that has no dna sequence?
perl
genome
genbank
updated 2.8 years ago by
Ram
44k • written 10.0 years ago by
fr
▴ 220
4
votes
6
replies
3.3k
views
How to debug (and solve) Bioperl problems when a gbk file doesn't have the genome?
bioperl
genbank
NCBI
updated 3.0 years ago by
Ram
44k • written 10.2 years ago by
fr
▴ 220
8
votes
11
replies
3.5k
views
BioPerl retrieves joined sequence incorrectly
genome
perl
bioperl
gene
cds
updated 3.8 years ago by
Ram
44k • written 10.3 years ago by
fr
▴ 220
0
votes
4
replies
3.7k
views
How to retrieve information from NCBI/genome with Perl?
perl
ncbi
updated 10.3 years ago by
Biostar
20 • written 10.4 years ago by
fr
▴ 220
1
vote
4
replies
2.7k
views
Database of Multicellular and Unicellular organisms
genome
unicellular
perl
databases
multicellular
updated 3.2 years ago by
Ram
44k • written 10.6 years ago by
fr
▴ 220
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