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Showing :
questions
0
votes
2
replies
239
views
How to convert Mummer coords output to a Bed file?
nucmer
mummer
bed
updated 6 weeks ago by
Ram
43k • written 6 weeks ago by
Biologist
▴ 290
0
votes
2
replies
798
views
Why FindMarkers between conditions shows pct.1 and pct.2 as 1 for most of the genes?
seurat
FindMarkers
scRNA-seq
updated 9 months ago by
Ram
43k • written 9 months ago by
Biologist
▴ 290
3
votes
3
replies
778
views
gtf2bed doesn't give gene_id in the bed file
rnaseq
gtf
bed
updated 19 months ago by
stolarek.ir
▴ 700 • written 19 months ago by
Biologist
▴ 290
1
vote
3
replies
1.7k
views
How to extract required lines of particular chromosome from a gtf file?
RNA-Seq
gtf
linux
command
updated 3.4 years ago by
Ram
43k • written 3.4 years ago by
Biologist
▴ 290
0
votes
6
replies
4.7k
views
Error with snakemake
snakemake
python
pipeline
salmon
updated 3.7 years ago by
Biostar
20 • written 5.8 years ago by
Biologist
▴ 290
0
votes
1
reply
689
views
Problem with edgesfile into cytoscape for network plot
RNA-Seq
wgcna
r
cytoscape
updated 3.8 years ago by
andres.firrincieli
3.6k • written 3.8 years ago by
Biologist
▴ 290
2
votes
14
replies
1.7k
views
Problem with differential analysis between two groups having low raw counts
RNA-Seq
edger
differential analysis
expression
updated 3.9 years ago by
ATpoint
81k • written 3.9 years ago by
Biologist
▴ 290
2
votes
6
replies
3.8k
views
How to get different outputs for kallisto on multiple samples?
kallisto
RNA-Seq
geneexpression
slurm
sbatch
updated 4.1 years ago by
swbarnes2
14k • written 4.1 years ago by
Biologist
▴ 290
1
vote
12
replies
4.1k
views
WGCNA: Problem with selecting soft threshold
RNA-Seq
wgcna
r
network
threshold
4.1 years ago by
Biologist
▴ 290
4
votes
13
replies
5.2k
views
Stringtie with Gencode gtf file doesn't give any gene_ids or transcript_ids?
RNA-Seq
stringtie
lncRNA
gtf
gencode
updated 4.3 years ago by
yiren
▴ 10 • written 6.2 years ago by
Biologist
▴ 290
1
vote
3
replies
950
views
Any R package to check the expression of single gene in multiple cancer types of TCGA?
RNA-Seq
tcga
r
geneexpression
updated 4.5 years ago by
Kevin Blighe
87k • written 4.5 years ago by
Biologist
▴ 290
12
votes
22
replies
4.6k
views
Classifying the samples based on zscore of a specific gene
RNA-Seq
R
geneexpression
zscore
4.5 years ago by
Biologist
▴ 290
0
votes
1
reply
749
views
How to check the expression of a gene using the sequence of that gene?
RNA-Seq
lncrna
sequence
blat
ensembl
updated 4.7 years ago by
flogin
▴ 280 • written 4.7 years ago by
Biologist
▴ 290
3
votes
5
replies
12k
views
How to convert featureCounts to FPKM?
RNA-Seq
featurecounts
fpkm
r
updated 5.0 years ago by
Ahmed Alhendi
▴ 230 • written 5.5 years ago by
Biologist
▴ 290
1
vote
3
replies
4.1k
views
Why median is NA for some of the group outcomes in survival analysis?
RNA-Seq
survival
kaplan-meier
clinical
r
updated 5.0 years ago by
Jean-Karim Heriche
27k • written 5.0 years ago by
Biologist
▴ 290
3
votes
7
replies
6.7k
views
6 follow
How to make a plot with gProfileR results?
RNA-Seq
gprofiler
geneexpression
pathways
plot
updated 5.0 years ago by
hedi.peterson
▴ 30 • written 5.4 years ago by
Biologist
▴ 290
3
votes
4
replies
2.9k
views
Error in differential analysis for samples with different time points
RNA-Seq
r
edger
differential analysis
updated 5.0 years ago by
h.mon
35k • written 5.0 years ago by
Biologist
▴ 290
6
votes
6
replies
4.4k
views
Estimating gene set enrichment using Fishers exact test
RNA-Seq
lncrna
gsea
fisherstest
5.1 years ago by
Biologist
▴ 290
12
votes
15
replies
2.6k
views
Pick soft threshold for co-expression analysis and filtering step
RNA-Seq
wgcna
coexpression
r
network
updated 5.2 years ago by
Kevin Blighe
87k • written 5.2 years ago by
Biologist
▴ 290
4
votes
14
replies
3.3k
views
Differential analysis with microarray data without idat or cel files
R
microarray
differential analysis
gene expression
updated 5.3 years ago by
Biostar
20 • written 5.4 years ago by
Biologist
▴ 290
8
votes
6
replies
2.8k
views
Significant pathways need to based on pvalue or adjusted pvalue or q-value?
r
RNA-Seq
clusterprofiler
pathways
updated 5.3 years ago by
ATpoint
81k • written 5.3 years ago by
Biologist
▴ 290
4
votes
4
replies
1.1k
views
Where Can I find protein-protein interactions data ?
RNA-Seq
protein
interactions
correlation
updated 5.4 years ago by
vkkodali_ncbi
★ 3.7k • written 5.4 years ago by
Biologist
▴ 290
5
votes
6
replies
4.1k
views
How to make an Oncoprint for a single gene in R?
RNA-Seq
oncoprint
plotting
geneexpression
updated 5.4 years ago by
Kevin Blighe
87k • written 5.4 years ago by
Biologist
▴ 290
6
votes
4
replies
4.0k
views
Spearman correlation between between two genes
RNA-Seq
correlation
spearman
geneexpression
updated 5.5 years ago by
Alex Reynolds
35k • written 5.5 years ago by
Biologist
▴ 290
4
votes
7
replies
3.6k
views
Is logCPM expression data good for plottinng?
RNA-Seq
R
geneexpression
plotting
edger
5.5 years ago by
Biologist
▴ 290
4
votes
4
replies
4.1k
views
Plot to show expression of a gene between two groups
RNA-Seq
r
gene expression
plot
updated 5.5 years ago by
EagleEye
7.5k • written 5.5 years ago by
Biologist
▴ 290
5
votes
4
replies
6.0k
views
Z-score calculation from raw counts data
RNA-Seq
heatmap
zscore
logcpm
updated 5.5 years ago by
Michael
54k • written 5.5 years ago by
Biologist
▴ 290
6
votes
10
replies
7.3k
views
Gene set enrichment analysis with edgeR output
RNA-Seq
gsea
edger
genesetenrichment
R
updated 5.5 years ago by
h.mon
35k • written 5.5 years ago by
Biologist
▴ 290
3
votes
12
replies
2.9k
views
Does FDR value change based Fold change cutoff?
RNA-Seq
edgeR
r
differential expression
statistics
updated 5.5 years ago by
Ram
43k • written 5.8 years ago by
Biologist
▴ 290
2
votes
3
replies
1.9k
views
p-value with chi-square test
RNA-Seq
statistics
p-value
significant test
r
updated 5.6 years ago by
Kevin Blighe
87k • written 5.6 years ago by
Biologist
▴ 290
7
votes
8
replies
3.2k
views
Survival plot between low and high expression of gene
RNA-Seq
r
survival
geneexpression
updated 5.6 years ago by
Santosh Anand
5.7k • written 5.6 years ago by
Biologist
▴ 290
0
votes
4
replies
2.2k
views
Why survival plots look different with same data?
RNA-Seq
tcga
survival
fpkm
survivalanalysis
updated 5.6 years ago by
Friederike
8.9k • written 5.6 years ago by
Biologist
▴ 290
4
votes
4
replies
3.2k
views
How to make a survival plot for a gene between High expression and low expression samples?
RNA-Seq
R
survival
plot
tcga
5.7 years ago by
Biologist
▴ 290
10
votes
18
replies
3.7k
views
How to construct Co-expression network between Coding and lncRNAs?
RNA-Seq
correlation
lncrna
co-expression network
r
updated 2.9 years ago by
Kevin Blighe
87k • written 5.7 years ago by
Biologist
▴ 290
5
votes
22
replies
3.3k
views
Differential analysis between two cell lines
R
RNA-Seq
edgeR
differential analysis
5.7 years ago by
Biologist
▴ 290
5
votes
12
replies
2.0k
views
How to make scatterplot with two different results sets?
RNA-Seq
r
scatterplot
plotting
updated 5.7 years ago by
zx8754
11k • written 5.7 years ago by
Biologist
▴ 290
2
votes
6
replies
1.4k
views
Differential analysis show different results
RNA-Seq
clustering
expression
rna-seq
gene
5.8 years ago by
Biologist
▴ 290
1
vote
5
replies
3.5k
views
stringtie merged gtf doesn't give any gene expression columns
RNA-Seq
stringtie
hisat2
merge
updated 5.9 years ago by
Kevin Blighe
87k • written 5.9 years ago by
Biologist
▴ 290
2
votes
6
replies
4.9k
views
How to make the script work with stringtie command first and then merge the outputs?
RNA-Seq
stringtie
merge
bash
linux
updated 6.0 years ago by
h.mon
35k • written 6.0 years ago by
Biologist
▴ 290
9
votes
19
replies
3.7k
views
Error in extracting Counts from the bam file using htseq-count
RNA-Seq
htseq
counts
bam
updated 6.1 years ago by
h.mon
35k • written 6.1 years ago by
Biologist
▴ 290
0
votes
1
reply
1.4k
views
script to write the path of all the output files of Cufflinks in a text file for Cuffmerge?
RNA-Seq
cuffmerge
cufflinks
updated 6.2 years ago by
Arup Ghosh
3.2k • written 6.2 years ago by
Biologist
▴ 290
3
votes
11
replies
3.3k
views
Identifying differentially expressed lncRNA's from RNA-Seq data
RNA-Seq
lncrna
ngs
updated 6.3 years ago by
Devon Ryan
104k • written 6.3 years ago by
Biologist
▴ 290
1
vote
1
reply
4.8k
views
How to cluster the annotation in the heat map?
r
heatmap
clustering
rna-seq
updated 6.5 years ago by
Kevin Blighe
87k • written 6.5 years ago by
Biologist
▴ 290
6
votes
21
replies
3.7k
views
How to make a color plot out of three columns from a dataframe in R?
r
heatmap
plot
6.9 years ago by
Biologist
▴ 290
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