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432 results • Page
4 of 9
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Views
Votes
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0
votes
5
replies
371
views
Telescope issue
Telescope
RNA-seq
updated 4 days ago by
GenoMax
142k • written 5 days ago by
eleven11
• 0
0
votes
6
replies
370
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
Erina
• 0
0
votes
0
replies
366
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
18 days ago by
Ronin
• 0
1
vote
5
replies
363
views
samtools filtering
samtools
updated 24 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
sansan_96
▴ 80
0
votes
4
replies
363
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
20 days ago by
pablo
▴ 300
0
votes
4
replies
358
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 24 days ago by
GenoMax
142k • written 27 days ago by
Soohyun
• 0
2
votes
4
replies
355
views
SnpEff annotates coding duplication as intronic?
snpeff
19 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
349
views
GSEA analysis in R
GSEA
R
Arabidopsis
18 days ago by
Sudip
• 0
0
votes
3
replies
348
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 23 days ago by
ATpoint
82k • written 24 days ago by
gdfsnkfns
• 0
3
votes
7
replies
347
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
6 days ago by
salias
• 0
0
votes
4
replies
342
views
Questions about transfering wgs file to reference genome file
fasta
cram
genome
24 days ago by
me
• 0
2
votes
4
replies
340
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
12 days ago by
samuelkalandarov2002
▴ 10
0
votes
3
replies
340
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 6 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
2
replies
339
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 20 days ago by
Istvan Albert
100k • written 22 days ago by
Jiang
• 0
1
vote
6
replies
338
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 2 days ago by
GenoMax
142k • written 20 days ago by
eebloom
▴ 80
0
votes
2
replies
335
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
22 days ago by
O.rka
▴ 710
0
votes
3
replies
325
views
Highest variable features in single cell data
single-cell
updated 9 days ago by
bk11
★ 2.4k • written 11 days ago by
carolofharvest
▴ 30
2
votes
4
replies
319
views
Addmetadata to seurat obj
seurat
25 days ago by
synat.keam
▴ 100
0
votes
2
replies
318
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
19 days ago by
Koketso
• 0
0
votes
0
replies
318
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
11 days ago by
pramach1
▴ 40
2
votes
2
replies
315
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 11 days ago by
Ram
43k • written 12 days ago by
v.berriosfarias
▴ 140
1
vote
3
replies
312
views
some error in building kraken2 database
metagenome
kraken2
12 days ago by
Art1ess
• 0
0
votes
1
reply
310
views
Monotonic genes in results of differential gene expression analysis
differential-expression
RNA-seq
monotonic-genes
updated 26 days ago by
Ram
43k • written 3 months ago by
Shaimaa Gamal
▴ 10
0
votes
1
reply
309
views
Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler
ortholog
sheep
updated 28 days ago by
Shuang He
• 0 • written 4 months ago by
Michael
• 0
1
vote
2
replies
308
views
Can I readmap short reads to rDNA references?
rDNA
assembly
updated 18 days ago by
Ram
43k • written 18 days ago by
aniigodwinn
• 0
1
vote
3
replies
307
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 7 days ago by
ATpoint
82k • written 8 days ago by
Francesco
▴ 10
1
vote
2
replies
305
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
19 days ago by
bp22
▴ 80
0
votes
1
reply
305
views
Could you please assist in identifying this cluster?
single-cell
updated 16 days ago by
Ram
43k • written 16 days ago by
carolofharvest
▴ 30
0
votes
2
replies
304
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 23 days ago by
Zhenyu Zhang
★ 1.2k • written 23 days ago by
Apollonia
• 0
0
votes
2
replies
304
views
bam merging for archaic samples
samtools
bam
updated 14 days ago by
Ram
43k • written 15 days ago by
Matteo Ungaro
▴ 100
0
votes
3
replies
303
views
How do I handle it if there are multiple ENSEMBL IDs in one gene symbol in the scRNA sequencing data?
Seurat
scRNA-seq
count-matrix
28 days ago by
Jeyong
• 0
1
vote
3
replies
300
views
True variants selection
vcf
bcftools
updated 23 days ago by
dthorbur
★ 1.9k • written 24 days ago by
maevalefeuvre
• 0
1
vote
2
replies
299
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
19 days ago by
bioinfo
▴ 150
0
votes
2
replies
298
views
RNAseq 1 control 2 different treatment
RNA-seq
19 days ago by
matteo.levorato
• 0
0
votes
4
replies
297
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
25 days ago by
njornet
▴ 20
0
votes
3
replies
293
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 5 days ago by
GenoMax
142k • written 6 days ago by
kim
• 0
0
votes
1
reply
292
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 18 days ago by
GenoMax
142k • written 18 days ago by
ycts
• 0
0
votes
2
replies
290
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
23 days ago by
ramin.k2013
• 0
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
4 days ago by
Nafi
• 0
2
votes
2
replies
289
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 24 days ago by
ATpoint
82k • written 24 days ago by
Shicheng Guo
★ 9.4k
2
votes
2
replies
289
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
20 days ago by
bioinfo
▴ 150
0
votes
3
replies
289
views
BLASTP web- <20aa peptides- interpreting results/ minimum E value?
blast
peptide
blastp
alignment
updated 24 days ago by
GenoMax
142k • written 24 days ago by
neish
• 0
0
votes
1
reply
287
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 16 days ago by
GenoMax
142k • written 16 days ago by
bioyas
▴ 10
0
votes
2
replies
287
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 19 days ago by
Ram
43k • written 20 days ago by
David
• 0
0
votes
2
replies
286
views
Annovar using R package
Annovar
gnomAD
R
10 days ago by
DKA
▴ 40
0
votes
1
reply
285
views
cibersort. problem
cibersort
gema122
updated 27 days ago by
Ram
43k • written 4 weeks ago by
gem1
• 0
0
votes
3
replies
284
views
KEGG Pathways
r
RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Sudip
• 0
0
votes
2
replies
283
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
18 days ago by
DKA
▴ 40
0
votes
0
replies
283
views
Different rsID for the same chromsome, position, ref & alt allele depending on different data sources. Which one should I use?
UKB
rsID
UKB-PPP
ensembl-vep
dbsnp
25 days ago by
lsy9
▴ 20
0
votes
2
replies
283
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
18 days ago by
mropri
▴ 150
432 results • Page
4 of 9
Recent Votes
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Association study using SNP data
.lgen file has 3+ different alleles
Force PLINK2 to neglect chrX as the sex chromosome
Answer: Force PLINK2 to neglect chrX as the sex chromosome
LD-prune variants while maintaining a list of SNPs
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Recent Replies
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
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snajafy
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I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata")
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11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata")
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82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata")
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You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
Comment: install package
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Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' removing 'C:/Users/najafi/AppData/…
Comment: Quetion regarding WGCNA
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3.6k
There is something wrong with your data but without any context I can't really answer to your question. I would like to see a PCA plot of …
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please could you tell me what was the solution, I am having the same problem, I only get empty files.
Comment: install package
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Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' * removing 'C:/Users/najafi/AppData…
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14k
Any chance the numerical columns were imported as factors?
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Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
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I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
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Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
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This worked beautifully using 'requests.get()' in python, thank you so much!
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