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120,583 results • Page
1 of 2412
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interpret ligand_receptor pairs
pairs
recepter
Ligand
multinichenetr
just now by
mayahammoud161
• 0
4
votes
7
replies
1.1k
views
DESeq2: error in checkFullRank(modelMatrix)
DESeqDataSet
design
DESeq2
RNA-Seq
updated just now by
Konrad
• 0 • written 3 months ago by
tilia
• 0
0
votes
0
replies
13
views
Comparability between normalized Counts / TPMs and log2FoldChange
FoldChange
TPMs
DESeq2
normalized
RNAseq
counts
50 minutes ago by
NorbertK
▴ 10
0
votes
1
reply
25
views
Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found
MuSiC2
updated 1 hour ago by
Bastien Hervé
6.1k • written 2 hours ago by
Pumla
• 0
0
votes
1
reply
39
views
Nanopore specific assembly tool of Mitochondria
Assembly
Nanopore
Mitochondria
updated 1 hour ago by
lieven.sterck
15k • written 2 hours ago by
adarsh_munna
▴ 60
2
votes
2
replies
172
views
Forum:
Do you agree with the practice of combing TCGA with GTEx?
GTEx
TCGA
updated 2 hours ago by
i.sudbery
21k • written 1 day ago by
nuorain
▴ 40
832
votes
169
replies
168k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
1
reply
196
views
Help with Funannotate
genomes
funannotate
fungus
annotation
updated 4 hours ago by
lieven.sterck
15k • written 3 days ago by
SomeOne
▴ 170
0
votes
0
replies
39
views
Annotations Tools
annotations
for
Tools
updated 2 hours ago by
GenoMax
149k • written 4 hours ago by
abebe1423
• 0
1
vote
1
reply
87
views
Alphafold in colab - homotrimer
Homotrimer
updated 30 minutes ago by
dthorbur
★ 2.9k • written 21 hours ago by
sjp24
• 0
0
votes
0
replies
27
views
peak calling for uneven readcounts
ATAC-seq
4 hours ago by
QX
▴ 70
1
vote
1
reply
222
views
News:
Final Call - Next-Generation Sequencing Data Analysis: A Practical Introduction (April 2-4 in Munich, Germany)
Workshop
RNAseq
Variant-Calling
Illumina
DNAseq
5 hours ago by
ecSeq Bioinformatics
▴ 10
0
votes
0
replies
46
views
Different results with 'clara-parabricks fq2bam' and bowtie2
fq2bam
clara-parabricks
fastq
bowtie2
8 hours ago by
Lars
• 0
0
votes
0
replies
45
views
GWAS to gene function prediction
annotation
vcf
gwas
prediction
gene
8 hours ago by
alnus
• 0
0
votes
2
replies
95
views
Adapters, adapters, adapters i´m so confused
miRNAs
GEO
Adpaters
miRNA-seq
Bioinformatics
updated 3 hours ago by
colindaven
7.2k • written 10 hours ago by
omicon
• 0
1
vote
2
replies
123
views
DEseq2: Advice for model (double interaction ?)
deseq2
matrix
dge
3 hours ago by
Picasa
▴ 650
0
votes
0
replies
67
views
Kallisto alignment with HPC (SLURM)
slurm
hpc
kallisto
alignment
15 hours ago by
tekica
• 0
0
votes
0
replies
68
views
KEGG pathways
KEGG
Pathways
17 hours ago by
Blue
• 0
2
votes
3
replies
343
views
Protein-Protein Network
Cytoscape
Genes
Breast-Cancer
Network
17 hours ago by
abdullah
• 0
0
votes
3
replies
204
views
Correct format for Hi-C matrix before converting to BEDPE
juicer
matrix
bedpe
HI-C
updated 20 hours ago by
kalavattam
▴ 320 • written 1 day ago by
desptsp
• 0
0
votes
0
replies
55
views
News:
Mass Spectrometry and Proteomics using R and Bioconductor course
R
Bioconductor
Mass-Spectrometry
Proteomics
updated 19 hours ago by
Ram
45k • written 21 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
98
views
How to download data from MGRAST
MGRAST
microbiome
metagenome
1 day ago by
Maxwell
▴ 50
0
votes
1
reply
178
views
Gene level expression versus variant-level expression
variant
RNASeq
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
ramiro.barrantes
▴ 20
0
votes
1
reply
127
views
Java error in BEAST2
BEAST2
java
updated 1 day ago by
Pierre Lindenbaum
165k • written 1 day ago by
Rafae
• 0
1
vote
10
replies
2.1k
views
Bedmethyl file format
bedmethyl
methylation
updated 22 hours ago by
lavigne
• 0 • written 10 months ago by
njornet
▴ 20
0
votes
3
replies
345
views
Tool:
PIASO, a python toolkit for single-cell data analysis
data-integration
scRNA-seq
normalization
scATAC-seq
spatial-transcriptomics
2 days ago by
Min
• 0
12
votes
6
replies
479
views
Forum:
What is the current state of the beef against UMAP/tSNE in the context of sc trajectory analysis/monocle3?
monocle3
umap
single-cell
tSNE
trajectory
2 days ago by
txema.heredia
▴ 210
0
votes
1
reply
266
views
Type of Pangenome Type/program to use for fungal isolates of the same species, but have major translocations
visualization
pangenome
genome
alignment
updated 1 day ago by
samuel.a.odonnell
▴ 590 • written 2 days ago by
Drew
• 0
0
votes
0
replies
130
views
Finding Indel Mutant structures
indel
2 days ago by
Logan
• 0
0
votes
0
replies
132
views
Doublet Detection for Intestinal Immune Cells in scRNA-seq
scDblFinder
Seurat
scRNA-seq
Doublets
Immune
2 days ago by
s
• 0
4
votes
7
replies
2.3k
views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated 2 days ago by
SanjidaR_NCBI
▴ 60 • written 17 days ago by
Bruno Santos
• 0
0
votes
1
reply
273
views
no "-" strand in transcriptome alignment
DRS
transcriptome
alignment
updated 2 days ago by
GenoMax
149k • written 6 days ago by
baibhu1234
▴ 20
0
votes
3
replies
241
views
What is best way to do CNV Analysis on Xenium data (Spatial transcriptomics)?
seurat
xenium
spatialtranscriptomics
singlecell
updated 2 days ago by
yura.grabovska
▴ 710 • written 3 days ago by
geno89
▴ 20
0
votes
0
replies
131
views
Background correction using MBCB (Illumina HT-12V4)
transcriptomics
2 days ago by
Ariadna
▴ 20
2
votes
3
replies
306
views
Finding a gene in human
variant
gene
updated 1 day ago by
GenoMax
149k • written 2 days ago by
zizigolu
★ 4.3k
3
votes
4
replies
273
views
Assigning cell annotation based on calculated scores.
Clustering
Seurat
UCell
cell-annotations
Score
updated 3 days ago by
ATpoint
87k • written 3 days ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
140
views
single cell rna seq NMF Error in which.min(sapply(res.runs, "[[", "residuals"))
error
sc-rna-seq
Seurat
NMF
updated 3 days ago by
Bastien Hervé
6.1k • written 3 days ago by
Beatriz
• 0
1
vote
1
reply
217
views
Low quality of NGS SNP analysis panel
fastqc
iontorrent
ngs
updated 3 days ago by
Prash
▴ 290 • written 3 days ago by
kate-nelis
• 0
2
votes
4
replies
554
views
Multiple fail points in fastqc file
fastqc
report
3 days ago by
dr.deepakkukkar
• 0
1
vote
1
reply
234
views
mapping to transcriptome.fasta vs genome.fasta
mapping
gtf
transcriptome
genome
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
baibhu1234
▴ 20
0
votes
1
reply
202
views
Where to find WGS, metagenome data for obesity group?
HMP
microbiome
data
NCBI
metagenomics
updated 3 days ago by
ATpoint
87k • written 3 days ago by
Emily
▴ 70
1
vote
2
replies
284
views
WDL 1.0 - Directory Type
directory
input
wdl
6 hours ago by
davidmaimoun
▴ 50
0
votes
0
replies
158
views
How to input INDELs in ped files
SNP
R
haplostats
Haploview
INDEL
3 days ago by
Ant
▴ 40
1
vote
0
replies
169
views
Tool:
HGVSV: A tool to parse and generate HGVS names with Structural Variant support
Variants
HGVSV
Variant
HGVS
Structural
3 days ago by
parker.payne
▴ 10
0
votes
3
replies
269
views
P-value calculation between groups in split violin plot
violinplot
ggplot
singlecellRnaseq
updated 3 days ago by
LChart
4.9k • written 3 days ago by
AB
▴ 390
0
votes
1
reply
471
views
Clumping- cannot mtfrm
clumping
MR
updated 3 days ago by
gongyuxu
• 0 • written 6 weeks ago by
sp
• 0
0
votes
2
replies
237
views
After doublet detection in 10x scRNA-Seq data, there is still evidence of doublets
R
DoubletFinder
Seurat
scRNA
updated 3 days ago by
fracarb8
★ 1.7k • written 3 days ago by
yura.grabovska
▴ 710
0
votes
0
replies
162
views
Hash-Based Allele Calling
calling
hash
allele
4 days ago by
davidmaimoun
▴ 50
3
votes
1
reply
213
views
VCF filtering with Allele Balance (AB) using FilterVcf (Picard)
Picard
Allele
AB
Balance
GATK
FilterVcf
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
Eduardo
▴ 20
0
votes
0
replies
183
views
Issues with FPKM Calculation in RNA-seq Analysis (Apodemus agrarius)
FPKM.
Cufflinks
updated 4 days ago by
lieven.sterck
15k • written 4 days ago by
ohtang7
▴ 40
120,583 results • Page
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Answer: DESeq2: error in checkFullRank(modelMatrix)
by
Konrad
• 0
Wouldn't it be possible to model the nested structure by an interaction term (Phenotype:Genotype) as a workaround: ~ Phenotype + Phen…
Comment: Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found
by
Bastien Hervé
6.1k
https://github.com/xuranw/MuSiC/issues/3 Try : library(xbioc)
Comment: Nanopore specific assembly tool of Mitochondria
by
lieven.sterck
15k
why do you assume that Flye would not work here? I don't have any in mind immediately but perhaps look for a plasmid assembler with ONT da…
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by
i.sudbery
21k
Your friends are right. You cannot remove batch effects when the batch effect is confounded with the biological condition of interest. remo…
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7.2k
I would only add that it often makes sense to do several rounds of adapter trimming, and check (eg with fastqc) that no adapters remain. Th…
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Picasa
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Thanks for your advice. I will try this
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why are you using `*.proteins.fa` as input for interpro? do yo have the proteins in several files then? Can you check the interpro config …
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15k
1) no, if you ran it within Interproscan it should be OK. (keep in mind you will need to configure interproscan to include this analysis) …
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lieven.sterck
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that certainly is an option indeed. Just running a blast against nr-prot DB of NCBI and investigating the best hit(s) is a way to go (bit c…
Answer: Alphafold in colab - homotrimer
by
dthorbur
★ 2.9k
Yes, you have it correct. Just add the sequence to a fasta delimiting the each chain with a colon. `example.fasta` would look like: ``` >…
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by
ecSeq Bioinformatics
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Final Call - Some last seats available! Apply Now!
Comment: WDL 1.0 - Directory Type
by
davidmaimoun
▴ 50
Thank you very much Sam, it is working! Have a good day
Comment: sliding windows over genome
by
cmdcolin
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the fai file generated by samtools faidx basically has this. the first two columns of yourfile.fa.fai are "chromosome name" "length of chro…
Answer: Adapters, adapters, adapters i´m so confused
by
GenoMax
149k
While illumina adapter sequences are easy to find (there is a PDF you can look for on net), miRNA adapters are specific for kit being used.…
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