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questions
0
votes
4
replies
779
views
Boxplot of contrasts and genes together
boxplot
deseq2
expression
updated 10 months ago by
Papyrus
★ 2.9k • written 10 months ago by
bioinfo8
▴ 230
12
votes
8
replies
3.7k
views
DESeq2 design for two variables and pairwise comparisons
deseq2
contrasts
rnaseq
LRT
updated 2.1 years ago by
1769mkc
★ 1.2k • written 3.0 years ago by
bioinfo8
▴ 230
5
votes
5
replies
4.5k
views
How can I make boxplot for a single gene from one of the contrasts generated by limma?
limma
microarray
contrasts
boxplot
updated 4.4 years ago by
Gordon Smyth
★ 7.1k • written 4.5 years ago by
bioinfo8
▴ 230
0
votes
1
reply
2.5k
views
CoverageView package_Error in 1:nrow(grDF) : argument of length 0
CoverageView
R
bioconductor
mclapply
updated 5.7 years ago by
KatjaS
▴ 10 • written 6.9 years ago by
bioinfo8
▴ 230
5
votes
6
replies
5.9k
views
Convert gff3 to gtf with R or shell
R
ngs
shell
gff3
gtf
5.8 years ago by
bioinfo8
▴ 230
0
votes
1
reply
4.4k
views
Extract gene ids from DESeq2 result dataframe for specific comparison based on vennDiagram
deseq2
vennDiagram
RNA-Seq
limma
venn
updated 6.4 years ago by
Kevin Blighe
87k • written 6.4 years ago by
bioinfo8
▴ 230
14
votes
7
replies
7.2k
views
Sleuth: Combined lrt and wt tests, clustered heatmap
RNA-Seq
Sleuth
kallisto
R
heatmap
updated 6.5 years ago by
erdiazval
▴ 110 • written 7.4 years ago by
bioinfo8
▴ 230
1
vote
3
replies
3.3k
views
Error while running clusterProfiler
clusterProfiler
RNA-Seq
R
updated 6.5 years ago by
Guangchuang Yu
★ 2.6k • written 6.5 years ago by
bioinfo8
▴ 230
6
votes
3
replies
10k
views
featureCounts for paired bam files and dealing with multimapping reads?
featureCounts
paired
multimapping reads
RNA-Seq
updated 6.5 years ago by
Devon Ryan
104k • written 6.5 years ago by
bioinfo8
▴ 230
10
votes
10
replies
3.5k
views
DNA sequence of genes from vcf file
vcf
variant calling
gene
bcftools
ensembl
updated 6.6 years ago by
songbaoxing168
• 0 • written 6.8 years ago by
bioinfo8
▴ 230
0
votes
1
reply
3.3k
views
RSeQC installation error
ngs
QC
python
RSeQC
updated 6.6 years ago by
h.mon
35k • written 6.6 years ago by
bioinfo8
▴ 230
1
vote
4
replies
2.5k
views
Error in running QoRTs after hisat2 alignment
RNA-Seq
QoRTs
paired-end
samtools
java
updated 6.6 years ago by
h.mon
35k • written 6.6 years ago by
bioinfo8
▴ 230
2
votes
7
replies
2.7k
views
Whether to use all aligned reads (QC-passed) or only properly-paired reads from rnaseq data?
RNA-Seq
properly-paired
samtools
ngs
hisat2
6.6 years ago by
bioinfo8
▴ 230
4
votes
11
replies
2.6k
views
Error while running rnaseq_pipeline.sh provided by hisat2
hisat2
paired-end
RNA-Seq
bash
shell
6.6 years ago by
bioinfo8
▴ 230
2
votes
11
replies
3.4k
views
Extract consensus dna sequence of multiple genes from multiple bam files in fasta format
samtools
fasta
genes
bam
consensus
6.7 years ago by
bioinfo8
▴ 230
9
votes
24
replies
6.8k
views
Add filename to fasta headers of multiple fasta files inside loop
pyfasta
header
fasta
bash
gene
6.7 years ago by
bioinfo8
▴ 230
2
votes
12
replies
3.5k
views
convert bam to clustal
alignment
bam
clustal
R
bioconductor
6.7 years ago by
bioinfo8
▴ 230
2
votes
4
replies
2.0k
views
Retrieval of similar positions from samples in a vcf but different from reference
vcf
bcftools
variant calling
updated 6.7 years ago by
guillaume.rbt
★ 1.0k • written 6.7 years ago by
bioinfo8
▴ 230
2
votes
3
replies
1.7k
views
Retain file names as sample names while making pileup
vcf
variant calling
bcftools
gene
samtools
updated 6.8 years ago by
WouterDeCoster
47k • written 6.8 years ago by
bioinfo8
▴ 230
2
votes
7
replies
4.2k
views
Compute inner mate distance for paired-end reads in a bam file
picard
bam
paired
updated 6.9 years ago by
Devon Ryan
104k • written 6.9 years ago by
bioinfo8
▴ 230
18
votes
22
replies
11k
views
Samtools: How can I extract properly-paired QC-passed reads instead of extracting only properly-paired?
samtools
bam
ngs
sequencing
paired-end
6.9 years ago by
bioinfo8
▴ 230
0
votes
0
replies
1.2k
views
TEQC (Target Enrichment Quality Control, R package) : Clarification on paired-end reads
TEQC
paired-end
R
bioconductor
ngs
6.9 years ago by
bioinfo8
▴ 230
0
votes
1
reply
2.4k
views
Error: Pathway analysis using Sleuth results
RNA-Seq
Sleuth
GAGE
Pathview
R
updated 7.0 years ago by
bigmawen
▴ 430 • written 7.4 years ago by
bioinfo8
▴ 230
1
vote
0
replies
1.9k
views
transcript to gene mapping after sleuth run
sleuth
kallisto
RNA-Seq
R
biomaRt
7.0 years ago by
bioinfo8
▴ 230
8
votes
9
replies
2.8k
views
Convert fasta to bed (no gtf available)
genome
ensembl
bed
fasta
CDS
7.0 years ago by
bioinfo8
▴ 230
7
votes
8
replies
3.0k
views
Convert cds .fa to bed
ensembl
bed
fasta
cds
ucsc
7.0 years ago by
bioinfo8
▴ 230
2
votes
2
replies
4.8k
views
Rstudio server on Ubuntu 16.04.2 LTS, RStudio initialization error: unable to connect to service
rstudio server
r
ubuntu
rstudio
7.2 years ago by
bioinfo8
▴ 230
8
votes
12
replies
2.1k
views
Whole exomes: comparative analysis
exome
R
whole exome
BAM
7.2 years ago by
bioinfo8
▴ 230
0
votes
7
replies
2.3k
views
Whole exomes: Rsamtools, RAM issue
R
Rsamtools
whole exome
RAM
BAM
7.2 years ago by
bioinfo8
▴ 230
2
votes
5
replies
3.1k
views
Character matrix to Numeric matrix for heatmap
RNA-Seq
R
next-gen
sleuth
7.4 years ago by
bioinfo8
▴ 230
0
votes
1
reply
1.2k
views
kallisto to metaseqR
kallisto
RNA-Seq
R
next-gen
7.4 years ago by
bioinfo8
▴ 230
6
votes
8
replies
3.1k
views
percentage of amino acids, normalize by background amino acid probability
Amino acid
percentage
normalization
excel
updated 8.2 years ago by
abascalfederico
★ 1.2k • written 8.2 years ago by
bioinfo8
▴ 230
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