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170 results • Page
2 of 4
Sort: Views
Rank
Views
Votes
Replies
2
votes
2
replies
309
views
Association study using SNP data
Association
Allele
Parentage
SNP
2 days ago by
drajangirija
• 0
0
votes
6
replies
303
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 4 days ago by
dsull
★ 6.0k • written 5 days ago by
Chen
• 0
0
votes
0
replies
294
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
4 days ago by
NorbertK
• 0
0
votes
1
reply
295
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 1 day ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
1
vote
2
replies
293
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
6 days ago by
Nafi
• 0
2
votes
1
reply
291
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 3 days ago by
chrchang523
10k • written 7 days ago by
8armed
▴ 10
0
votes
4
replies
289
views
HCL database download
database
HCL
human
updated 9 hours ago by
GenoMax
142k • written 3 days ago by
sooni
▴ 20
1
vote
3
replies
285
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Qi
• 0
1
vote
3
replies
282
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
1 day ago by
Dora
▴ 10
2
votes
3
replies
281
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 4 days ago by
dthorbur
★ 1.9k • written 4 days ago by
Vijith
▴ 30
1
vote
2
replies
281
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
4 days ago by
eebloom
▴ 80
5
votes
5
replies
280
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 5 days ago by
atharvakarkare14
▴ 30 • written 5 days ago by
Begonia_pavonina
▴ 150
0
votes
1
reply
279
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 5 days ago by
Scooter
▴ 280 • written 12 days ago by
avocado123
• 0
2
votes
2
replies
278
views
p-value in CIBERSORT
CIBERSORT
p-value
6 days ago by
michelafrancesconi9
▴ 20
1
vote
5
replies
277
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 1 day ago by
Ram
43k • written 1 day ago by
snajafy
• 0
3
votes
5
replies
277
views
Generating mpileup file using samtools
mpileup
samtools
updated 4 days ago by
Joe
21k • written 4 days ago by
Ruqaiya
• 0
1
vote
3
replies
273
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
2 days ago by
Lada
▴ 30
1
vote
2
replies
273
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
1 day ago by
M.
▴ 30
1
vote
3
replies
262
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 4 days ago by
Alex Reynolds
35k • written 5 days ago by
SJP
• 0
0
votes
5
replies
255
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 1 hour ago by
Ram
43k • written 1 day ago by
JACKY
▴ 140
1
vote
2
replies
253
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
5 days ago by
rianna.collins
• 0
0
votes
1
reply
252
views
creating batch colum for batch correction
batch-correction
combat
1 day ago by
Expert
▴ 10
4
votes
2
replies
250
views
GRCh38.gmap file
gnomix
gmap
2 days ago by
lorena9132
▴ 10
0
votes
2
replies
245
views
Downloading older version of a tool
Alignment
tools
3 days ago by
Ruqaiya
• 0
0
votes
2
replies
239
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 1 day ago by
GenoMax
142k • written 2 days ago by
mropri
▴ 150
1
vote
3
replies
241
views
Odd alignment question/finding
Alignment
updated 4 days ago by
barslmn
★ 2.1k • written 5 days ago by
poordumbsillyidiot
• 0
1
vote
2
replies
240
views
RNA-seq data for deep learning classification
rna-seq
4 days ago by
yahn
• 0
1
vote
3
replies
236
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 5 days ago by
jared.andrews07
★ 16k • written 5 days ago by
yvonneh
▴ 10
1
vote
4
replies
232
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
2 hours ago by
heelpPlease
• 0
1
vote
2
replies
231
views
Downloading full alignments from Pfam
pfam
2 days ago by
bef1
• 0
0
votes
1
reply
229
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Thanujay S
• 0 • written 4 days ago by
yahn
• 0
3
votes
2
replies
229
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 3 days ago by
Ram
43k • written 4 days ago by
carolofharvest
▴ 30
0
votes
1
reply
229
views
Subsetting and merging back Seurat Object brings different results
Seurat
5 days ago by
Bine
▴ 60
0
votes
2
replies
228
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
8 hours ago by
Ahiad Chen Zion
• 0
0
votes
2
replies
225
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
1 day ago by
kalavattam
▴ 190
0
votes
1
reply
223
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 6 days ago by
Adam
▴ 30 • written 7 days ago by
J
• 0
2
votes
2
replies
223
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
1 day ago by
brandon
• 0
4
votes
1
reply
223
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 1 day ago by
zx8754
11k • written 3 days ago by
Jautis
▴ 560
3
votes
3
replies
221
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
15 hours ago by
Adyasha
• 0
2
votes
2
replies
213
views
Raw counts using stringtie
stringtie
RNA-seq
updated 4 days ago by
GenoMax
142k • written 4 days ago by
ahmad.sajad4541
• 0
0
votes
1
reply
208
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 5 days ago by
GenoMax
142k • written 6 days ago by
mgranada3
▴ 30
0
votes
1
reply
207
views
Help with DGEList function
DGEList
R
updated 2 days ago by
marco.barr
▴ 90 • written 3 days ago by
Natali
• 0
0
votes
1
reply
203
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 3 days ago by
Ram
43k • written 4 days ago by
Rob
▴ 170
0
votes
2
replies
201
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
1 hour ago by
sainavyav22
• 0
0
votes
2
replies
196
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
5 days ago by
dtnondorf
• 0
0
votes
1
reply
195
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ximena
• 0
1
vote
2
replies
193
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 11 hours ago by
Weiwen
• 0 • written 1 day ago by
MICOS
▴ 10
1
vote
0
replies
189
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
189
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 6 days ago by
i.sudbery
19k • written 6 days ago by
Edmond
• 0
0
votes
1
reply
188
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 3 days ago by
Ram
43k • written 4 days ago by
Valentina
• 0
170 results • Page
2 of 4
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq
by
robert.flynn.21
• 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
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