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1,000 results • Page
4 of 20
Sort: Views
Rank
Views
Votes
Replies
1
vote
7
replies
8.8k
views
How single sample GSEA works
ssgsea
RNA-seq
R
GSVA
updated 4.8 years ago by
Kevin Blighe
88k • written 4.8 years ago by
sugus
▴ 150
4
votes
16
replies
8.8k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.7 years ago by
Biostar
20 • written 7.5 years ago by
lu.ne
▴ 70
5
votes
24
replies
8.7k
views
Plink1.9 gives error when converting VCF.gz to PED? "Error read failure"
VCF
Plink
5.9 years ago by
DanielC
▴ 170
2
votes
9
replies
8.7k
views
How to highlight genes on a Manhattan plot
R
gene
SNP
updated 2.4 years ago by
Ram
43k • written 9.8 years ago by
kyoko777
• 0
18
votes
4
replies
8.7k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 14 months ago by
Ram
43k • written 10.8 years ago by
user
▴ 940
5
votes
17
replies
8.7k
views
Removing fastq duplicates
sequence
next-gen
ChIP-Seq
3.5 years ago by
C4
▴ 30
1
vote
7
replies
8.6k
views
merge two SeuratObjects to do the integration
RNA-Seq
3.8 years ago by
yueli7
▴ 250
5
votes
4
replies
8.6k
views
GFF3 to GTF conversion - 9th column
gtf
NCBI
gff3
featureCounts
updated 21 months ago by
Ram
43k • written 8.3 years ago by
mrodrigues.fernanda
▴ 50
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap
RNA-Seq
clustering
5.1 years ago by
CuriousGuy
▴ 90
2
votes
7
replies
8.6k
views
Design matrix not of full rank.
RNA-Seq
edgeR
R
7.9 years ago by
firestar
★ 1.6k
7
votes
18
replies
8.6k
views
9 follow
Cuffmerge running error
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.5 years ago by
hana
▴ 190
0
votes
1
reply
8.5k
views
Purpose Of Y-Shaped Adapters In Illumina Sequencing?
illumina
adaptor
sequencing
rna-seq
11.0 years ago by
gaelgarcia05
▴ 280
1
vote
2
replies
8.5k
views
vcf compare between 2 vcf files using vcf tools
vcftools
updated 14 months ago by
Ram
43k • written 7.5 years ago by
bioguy24
▴ 230
2
votes
8
replies
8.5k
views
STAR mapping results
RNA-Seq
updated 4.5 years ago by
Biostar
20 • written 4.7 years ago by
mxlsherry1992
▴ 80
6
votes
15
replies
8.5k
views
Strand specific protocol for bowtie2 alignment
bowtie2
rnaseq
alignment
RNA-Seq
updated 2.5 years ago by
Ram
43k • written 8.5 years ago by
nalandaatmi
▴ 100
10
votes
6
replies
8.5k
views
Any idea how to solve this error in fgsea - "Error in if (any(simpleFgseaRes$modeFraction < 10)) { : missing value where TRUE/FALSE needed"?
fgsea
updated 2.9 years ago by
alserg
▴ 930 • written 2.9 years ago by
gabrielbaldanzi
▴ 10
0
votes
7
replies
8.4k
views
Bio-DB-HTS installation and ensembl-vep
Bio-DB-HTS
ensembl
vep
updated 2.7 years ago by
al.bodrug
▴ 50 • written 5.2 years ago by
felipead66
▴ 120
5
votes
20
replies
8.4k
views
How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
ChIP-Seq
homer
7.8 years ago by
varsha619
▴ 90
2
votes
9
replies
8.4k
views
Map ensembl gene id form hg38 in hg19
sequencing
hg38
hg19
7.9 years ago by
Tanvir Ahamed
▴ 350
1
vote
2
replies
8.4k
views
Awk- How to compare 2 files with common columns and then get the output file with columns from each file.
awk
7.6 years ago by
bright.g.january1732
• 0
5
votes
3
replies
8.4k
views
Differential Gene Expression (EdgeR?) : What are the steps in computing this?
gene
rna
microarray
differential
expression
7.8 years ago by
O.rka
▴ 720
3
votes
4
replies
8.3k
views
RNA-Seq raw fastq files from TCGA
RNA-Seq
TCGA
fastq
7.4 years ago by
oriolebaltimore
▴ 190
2
votes
7
replies
8.3k
views
linux 'cat' command merge fasta files without headers
fasta
linux
updated 14 months ago by
Ram
43k • written 9.9 years ago by
esterbuiate
• 0
4
votes
5
replies
8.3k
views
Calculating FPKM from HTSeq counts table
RNA-Seq
R
HTSeq
fpkm
6.7 years ago by
ann081993
▴ 10
0
votes
8
replies
8.2k
views
R providing row numbers instead row names with read.csv?
R
updated 4.0 years ago by
zx8754
11k • written 4.0 years ago by
blacktomato27
▴ 70
9
votes
11
replies
8.2k
views
8 follow
Extremely low mapping rates with bowtie2
alignment
next-gen
updated 6.6 years ago by
Biostar
20 • written 6.6 years ago by
Sachin
▴ 10
0
votes
3
replies
8.2k
views
adding PCA ellipses on ggplot2
gene
RNA-Seq
ggplot2
pca
5.6 years ago by
demoraesdiogo2017
▴ 100
1
vote
2
replies
8.2k
views
How To Compute A Genetic Map For Snps
plink
snp
updated 10.8 years ago by
Biostar
20 • written 11.2 years ago by
Tim
▴ 10
1
vote
4
replies
8.2k
views
Error when trying to install a package (non-zero exit status)
Packages
Bioconductor
updated 2.0 years ago by
jv
★ 1.8k • written 2.0 years ago by
BioC123
• 0
5
votes
1
reply
8.2k
views
*.rnk file preparation for GSEA analysis
RNA-Seq
GSEA
Enrichment analysis
R
webgestalt
4.7 years ago by
o.mikh90
▴ 30
0
votes
1
reply
8.2k
views
How to solve error 'Error in split.default(X, group) : first argument must be a vector' in RepeatExplorer
software error
ngs
R
8.0 years ago by
namratapatel183
▴ 10
24
votes
25
replies
8.2k
views
How to generate Beta diversity boxplot from phyloseq object?
phyloseq
beta diversity
metagenomics
3.8 years ago by
dpc
▴ 240
0
votes
2
replies
8.1k
views
How to solve error memory R package pedigree
pedigree
R
software error
memory
5.8 years ago by
Kian
▴ 50
0
votes
4
replies
8.1k
views
Problem With Autodock 4.2.5
docking
updated 2.2 years ago by
Ram
43k • written 11.4 years ago by
Dollas Salleh
▴ 70
2
votes
2
replies
8.1k
views
How to filter out special sequences from a fasta file based on sequence IDs txt
fasta
updated 20 months ago by
Ram
43k • written 8.6 years ago by
Ginsea Chen
▴ 130
6
votes
9
replies
8.1k
views
Why we need 100X coverage to get a high-quality assembly?
genome
Assembly
PacBio
Coverage
7.5 years ago by
lamz138138
▴ 40
5
votes
1
reply
8.1k
views
Meaning Of Colors Used In Samtools Tview
samtools
11.4 years ago by
deepthithomaskannan
▴ 380
7
votes
12
replies
8.1k
views
How to identify ORFs in Python dictionaries
Python3
ORF
Open reading frame
python dictionaries
7.3 years ago by
ron
▴ 40
2
votes
1
reply
8.0k
views
ROH by PLINK
plink
ROH
updated 15 months ago by
Ram
43k • written 9.0 years ago by
afadda
▴ 20
5
votes
14
replies
8.0k
views
Microrna Adapter Trimming
updated 10.5 years ago by
Fabio Marroni
★ 3.0k • written 10.5 years ago by
xiaojuhu13
▴ 150
2
votes
2
replies
8.0k
views
Is There A Website That Will Generate A Citation Or Collaboration Network For A Given Keyword(S) Or A Publication?
network
search
10.6 years ago by
Superbest
▴ 130
1
vote
4
replies
8.0k
views
Polygenic Risk Score PLINK
plink
polygenic risk score
risk score
SNP scoring
updated 6.2 years ago by
rse
▴ 100 • written 7.5 years ago by
mzezza
▴ 10
1
vote
3
replies
8.0k
views
Calling differential peaks on ATAC-seq data
ATAC-seq
THOR
MACS2
Peak Calling
updated 2.7 years ago by
117010004
• 0 • written 7.2 years ago by
ldyer2006
▴ 50
1
vote
7
replies
8.0k
views
Unaligned Reads From Bowtie2
bowtie2
updated 2.4 years ago by
Ram
43k • written 10.5 years ago by
deepthithomaskannan
▴ 380
4
votes
2
replies
8.0k
views
PLINK Merge error: File write failure
plink
1000genomes
updated 20 months ago by
Ram
43k • written 8.6 years ago by
aritra90
▴ 70
0
votes
4
replies
8.0k
views
Potential issue setting breaks in R for heatmap? Getting different results in RStudio's Plots panel than Exporting PDF
R
heatmap
Rstudio
updated 6.4 years ago by
Biostar
20 • written 6.6 years ago by
moldach
▴ 130
2
votes
4
replies
8.0k
views
Clustering data - data transformation (log2) highly improves clustering but why?
clustering
Elisa
data transformation
6.5 years ago by
JJ
▴ 680
2
votes
6
replies
8.0k
views
Heatmap using pheatmap issues
R
7.3 years ago by
1769mkc
★ 1.2k
1
vote
5
replies
7.9k
views
How To Retrieve Chromosome Lengths Using Bsgenome Package?
chromosome
length
10.6 years ago by
James Ashmore
▴ 100
4
votes
12
replies
7.9k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 3 months ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
1,000 results • Page
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Comment: GG Sankey plot
by
bk11
★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool
by
ntsopoul
▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool
by
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142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
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by
bk11
★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
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@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
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3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
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by
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For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
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Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
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I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
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