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1,000 results • Page
3 of 20
Sort: Views
Rank
Views
Votes
Replies
1
vote
4
replies
9.2k
views
R ggplot Align Y-Axis on multiple graphs
ggarrange
ggplot2
r
updated 4.1 years ago by
Biostar
20 • written 5.6 years ago by
jjrin
▴ 40
2
votes
2
replies
9.2k
views
Imputation Analysis In Plink?
plink
gwas
imputation
11.6 years ago by
Davy
▴ 210
4
votes
2
replies
9.2k
views
Hisat2 versus Bowtie2
Exome-sequencing
hisat2
bowtie2
updated 6.2 years ago by
Biostar
20 • written 7.4 years ago by
nalpas.nicolas
▴ 20
4
votes
10
replies
9.1k
views
Questions about multithreading of BWA
bwa
multithread
updated 5.0 years ago by
Ram
40k • written 7.6 years ago by
michealsmith
▴ 790
4
votes
6
replies
9.1k
views
Spades assembler output
Assembly
updated 14 months ago by
Ram
40k • written 7.7 years ago by
elbecerrasoto
▴ 30
3
votes
9
replies
9.1k
views
Random Forest returns "New factor levels not present in the training data"
R
Machine Learning
microarrays
5.6 years ago by
arronar
▴ 280
1
vote
7
replies
9.1k
views
How to find up-regulated and down-regulated genes after GEO2R analysis?
GEO
genes
up-regulated
down-regulated
GEO2R
5.6 years ago by
DanielC
▴ 160
4
votes
3
replies
9.1k
views
Convert Tab delimited file to VCF file
snp
updated 16 months ago by
Ram
40k • written 7.9 years ago by
niharraul
• 0
1
vote
6
replies
9.1k
views
How to use python to process .CEL file?
cel
affymetrix
python
R
cmap
updated 16 months ago by
Ram
40k • written 8.5 years ago by
zero_hsy
▴ 110
2
votes
2
replies
9.0k
views
Multiple whole genome alignment tools ?
multiple whole genome
alignment
4.3 years ago by
Picasa
▴ 640
5
votes
2
replies
9.0k
views
Turning Seq objects into strings
sequence
4.5 years ago by
schlogl
▴ 150
2
votes
4
replies
9.0k
views
num_threads with blastn in blast 2.6.0+
blast
4.8 years ago by
navela78
▴ 70
7
votes
5
replies
9.0k
views
strange issues with absent EOF markers in BAM files
samtools
picard-tools
bam
eof
7.3 years ago by
abascalfederico
★ 1.2k
3
votes
5
replies
8.9k
views
Using 'blastn' to do a remote search on NCBI BLAST against the nt collection database
blast
shell
unix
linux
5.6 years ago by
maciwuk
• 0
1
vote
6
replies
8.9k
views
Deseq2 : Filtering low counts before per sample
Deseq2
threshold-seq
4.9 years ago by
Cdk
• 0
0
votes
19
replies
8.9k
views
Skip orientation as there are not enough pairs by bwa mem
whole genome
bwa
paired end sequencing
4.3 years ago by
seta
★ 1.8k
0
votes
11
replies
8.8k
views
Error in installation R package
R
updated 7.0 years ago by
Biostar
20 • written 7.1 years ago by
niutster
▴ 110
5
votes
11
replies
8.8k
views
R- Kruskal-Wallis test on multiple columns at once
R
statistics
test
kruskal-Wallis
R-statistics
4.2 years ago by
mafernandez
• 0
2
votes
12
replies
8.8k
views
8 follow
michigan imputation server
conversion
michigan imputation server
updated 22 months ago by
Fazil
• 0 • written 5.6 years ago by
Teresa
▴ 20
1
vote
13
replies
8.8k
views
MDS Plot R
RNA-Seq
4.2 years ago by
BioBaby
▴ 20
3
votes
8
replies
8.8k
views
DiffBind: Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
R
DiffBind
ChIP-Seq
4.5 years ago by
msimmer92
▴ 300
2
votes
8
replies
8.8k
views
topTable in limma
limma
toptable
5.9 years ago by
AHW
▴ 80
11
votes
29
replies
8.8k
views
SummarizedExperiment nrow differs from ncol
DESeq2
SummarizedExperiment
updated 23 months ago by
Ram
40k • written 9.3 years ago by
Parham
★ 1.6k
7
votes
8
replies
8.7k
views
Removing rRNA and tRNA sequences using GTF files
RNA-Seq
7.2 years ago by
pixie@bioinfo
★ 1.5k
4
votes
1
reply
8.7k
views
Need help with heatmaps in R, how to draw select genes or selected pathway??
RNA-Seq
DESEQ2
R
heatmap
ontology
updated 7.0 years ago by
Biostar
20 • written 7.0 years ago by
marina.kimyr
▴ 20
3
votes
4
replies
8.7k
views
Design Pcr Primers To Uniquely Identify A Bacterial Strain
bacteria
pcr
updated 9.9 years ago by
Biostar
20 • written 10.0 years ago by
Eric Normandeau
11k
7
votes
8
replies
8.6k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 4 weeks ago by
Ram
40k • written 7.4 years ago by
nikelle.petrillo
▴ 110
3
votes
8
replies
8.6k
views
Quantile normalizing prior to or after TPM scaling?
RNAseq
normalization
updated 7 months ago by
Kevin Blighe
86k • written 5.8 years ago by
mforde84
★ 1.4k
10
votes
11
replies
8.6k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 16 months ago by
Ram
40k • written 8.5 years ago by
SheelS
▴ 40
1
vote
2
replies
8.6k
views
Problem in merging 1000G and cases in Plink
merge
duplicate snp
plink
triallelic
1000G
7.0 years ago by
fatima
▴ 20
3
votes
4
replies
8.6k
views
how to filter vcf file based on sample DP? vcf tools does not work
vcf-filtering
sample DP
6.5 years ago by
Ana
▴ 200
0
votes
4
replies
8.5k
views
ITCN 1.6 ImageJ Plugin
software error
updated 5.9 years ago by
Biostar
20 • written 7.0 years ago by
verma
▴ 30
1
vote
3
replies
8.5k
views
Htseq Count Finding No Feature
htseq
bacteria
gene-expression
10.5 years ago by
joaslucas
▴ 90
1
vote
2
replies
8.5k
views
Install Plink V1.07 on Mac
software error
7.1 years ago by
xaviera417
• 0
3
votes
7
replies
8.4k
views
6 follow
remote blast requires installation of taxdb database
blast
updated 4.3 years ago by
Varshney
▴ 20 • written 6.0 years ago by
hfan22
▴ 40
5
votes
10
replies
8.4k
views
GWAS - approximate odds ratio and standard error
GWAS
imputation
updated 6.0 years ago by
Kevin Blighe
86k • written 6.0 years ago by
alessandrotestori7
▴ 410
0
votes
4
replies
8.4k
views
How to install PLINK on linux/Mac-OS
genome
2.9 years ago by
giusdalt95
▴ 10
2
votes
2
replies
8.4k
views
Plot minor allele frequency distribution in R?
gwas
maf
R
7.4 years ago by
dam4l
▴ 190
2
votes
7
replies
8.4k
views
How to annotate TTS or TES
ChIP-Seq
TES
annotation
6.6 years ago by
Lila M
★ 1.2k
13
votes
13
replies
8.3k
views
How to do pca plot from .eigenval and .eigenvec files from Plink in R.
R
SNP
updated 5.6 years ago by
Devon Ryan
103k • written 5.6 years ago by
amitgourav.ghosh12
▴ 70
18
votes
4
replies
8.3k
views
How To Find Rna-Seq Data Of Published Papers?
geo
next-gen
RNA-seq
updated 7 months ago by
Ram
40k • written 10.1 years ago by
user
▴ 940
2
votes
8
replies
8.3k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 14 months ago by
zx8754
11k • written 2.6 years ago by
aradhana
• 0
2
votes
9
replies
8.3k
views
How to highlight genes on a Manhattan plot
R
gene
SNP
updated 21 months ago by
Ram
40k • written 9.1 years ago by
kyoko777
• 0
4
votes
16
replies
8.3k
views
STAR - genome indexes generation, genome file not created
RNA-Seq
star
updated 4.1 years ago by
Biostar
20 • written 6.9 years ago by
lu.ne
▴ 70
5
votes
12
replies
8.3k
views
ADMIXTURE: "Invalid chromosome code. Use integers!"
admixture
genome
6.6 years ago by
beneficii
▴ 60
3
votes
0
replies
8.3k
views
edgeR: how to make contrasts with makeContrasts
ngs
edgeR
makeContrasts
glm
dge
4.9 years ago by
m98
▴ 400
0
votes
1
reply
8.3k
views
Purpose Of Y-Shaped Adapters In Illumina Sequencing?
illumina
adaptor
sequencing
rna-seq
10.4 years ago by
gaelgarcia05
▴ 280
3
votes
13
replies
8.3k
views
Actually meaning of log2FoldChange, p-value & padj in DESeq2 results
RNA-Seq
DESeq2
differentially expressed genes
5.0 years ago by
hffqyd
▴ 10
2
votes
3
replies
8.3k
views
what is the detailed information of .amb .ann .bwt .pac .sa files generated by the BWA aligner?
alignment
BWA
.ann
.bwt
.sa
updated 5.6 years ago by
WouterDeCoster
47k • written 5.6 years ago by
lffu_0032
▴ 90
2
votes
7
replies
8.2k
views
Design matrix not of full rank.
RNA-Seq
edgeR
R
7.2 years ago by
firestar
★ 1.6k
1,000 results • Page
3 of 20
Recent Votes
How to identify 16s sequences from binning data(contigs)?
geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
Comment: Calculation of TMB on gene level
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
Comment: ATAC-seq troubleshoot - Just Noise
t2t human reference genome for RNA-seq
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Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
by
ATpoint
76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
To be more clear, I have RNAi data from depmap with different cell lines and I separated them into two groups according to their EGFR mutat…
Comment: ATAC-seq troubleshoot - Just Noise
by
ATpoint
76k
You have reads, so sequencing is obviously fine. This is how the banding should look: https://kb.10xgenomics.com/hc/article_attachments/360…
Comment: Program for Overlapping DMRs (Differentially Methylated Regions) Between Groups
by
Basti
★ 1.7k
Do not use excel for bioinformatics purposes, using R you could use GRanges objects to find overlaps between your regions : https://www.bio…
Answer: Saving the output of LD pruning from SNPRelate package as a new GDS file
by
Patrick
• 0
Thank you James for the response; My problem is only if I want to use the output of LD pruning in a different software, like STRUCTURE (to …
Answer: Average Coverage after Assembly (Spades)
by
taniapsduarte
• 0
Hi, I'm running into the same issue. Did you make it work? Or did you find an alternative method? Thanks!
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