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832 results • Page
5 of 17
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Views
Votes
Replies
6
votes
7
replies
623
views
cutadapt not trimming all adapters in PE Illumina sequencing
NGS
Illumina
cutadapt
6 days ago by
joe
▴ 470
0
votes
1
reply
212
views
Using multiple reference genomes for alignment in dorado?
dorado
basecall
ONT
alignment
updated 8 days ago by
GenoMax
140k • written 8 days ago by
gideonav
• 0
0
votes
1
reply
264
views
Automatic protein symmetry classification from PDB coordinates
pdb
symmetry
protein
updated 8 days ago by
Mensur Dlakic
★ 26k • written 9 days ago by
Kartik
• 0
1
vote
7
replies
392
views
'Invalid parameter' error to generate a count matrix using featurecounts
RNA-seq
featurecounts
updated 8 days ago by
GenoMax
140k • written 8 days ago by
Shay
• 0
0
votes
1
reply
289
views
Find out shared differentially expressed genes between two cell lines due to knockdown treatment
expression
RNA
differential
gene
seq
updated 8 days ago by
swbarnes2
14k • written 9 days ago by
Xinqi
• 0
8
votes
16
replies
5.2k
views
9 follow
visualize CNV data based on WGS
CNV
updated 8 days ago by
clealk
▴ 50 • written 6.2 years ago by
Bogdan
★ 1.4k
1
vote
1
reply
175
views
Seeking for edgeR TMM Normalization calcul example
tmm
edgeR
deseq2
updated 8 days ago by
jared.andrews07
★ 16k • written 8 days ago by
Picasa
▴ 640
0
votes
0
replies
191
views
Tool:
MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data Analysis and Visualization
microbiome
analysis
data
16S
5 days ago by
camillatafuro
• 0
0
votes
0
replies
136
views
Tool for power calculation in GWAS for quantative trait
trait
quantative
power
calculation
GWAS
8 days ago by
chevivien
▴ 90
1
vote
1
reply
279
views
Advice for genetic diversity stats analysis with both variant and variant sites
pi
diversity
vcf
genetics
updated 8 days ago by
dthorbur
★ 1.7k • written 8 days ago by
ekirsch
• 0
0
votes
1
reply
210
views
How to find and visualize expression level of a dataset?
r
updated 8 days ago by
BioinfGuru
★ 1.6k • written 9 days ago by
uveyik
• 0
1
vote
3
replies
252
views
How to validate the assembly completeness of unaligned reads ?
MaSuRCA
SPAdes
updated 8 days ago by
GenoMax
140k • written 8 days ago by
Sony
▴ 10
0
votes
3
replies
427
views
Maximum returned records using epost?
E-utilities
biopython
updated 8 days ago by
GenoMax
140k • written 5 weeks ago by
theclubstyle
▴ 40
0
votes
1
reply
187
views
PEAR seems to have sense to me
PEAR
updated 8 days ago by
GenoMax
140k • written 8 days ago by
ManuelDB
▴ 80
0
votes
1
reply
171
views
Interprete plot of dispersion estimation by DESeq2
dispersion
DEXseq
DESeq2
updated 8 days ago by
Pierre Lindenbaum
160k • written 8 days ago by
tien
▴ 10
2
votes
3
replies
240
views
Annotate genes from gtf file to vcf file
gtf
genomics
vcf
8 days ago by
QX
• 0
2
votes
3
replies
247
views
Read length distribution of whole genome sequnces of human
fastq
read
fastqc
8 days ago by
Yellapu
• 0
0
votes
1
reply
159
views
Adding gene to GRange objects with single base
GRanges
genomics
updated 8 days ago by
ATpoint
81k • written 9 days ago by
QX
• 0
2
votes
2
replies
222
views
Infering the cell composition from bulk RNA-seq data for mouse
RNA-seq
deconvolution
mouse
7 days ago by
feather-W
• 0
0
votes
2
replies
201
views
Gene set to perform GSVA
GSVA
9 days ago by
CTLong
▴ 90
6
votes
5
replies
336
views
How to find gene ids for Pfam ids?
Pfam
Gene
8 days ago by
WUSCHEL
▴ 750
2
votes
4
replies
311
views
Pearson correlation between Gene and clinical parameters
read-counts
Pearson-correlation
updated 8 days ago by
Shred
★ 1.4k • written 9 days ago by
Mary
• 0
0
votes
1
reply
224
views
Capped expression values in single cell RNAseq (Tabula Sapiens/scanpy/CellXGene)
scanpy
cellxgene
scRNA-seq
10x
normalisation
9 days ago by
matt.a.bennett25890
▴ 20
2
votes
1
reply
189
views
RNA-seq scaling the data for heatmap
RNA-seq
heatmap
scaling
updated 9 days ago by
matt.a.bennett25890
▴ 20 • written 9 days ago by
maplewj
▴ 10
3
votes
11
replies
411
views
bedToBigBed error, what am I doing wrong?
Homer
software-error
UCSC
updated 8 days ago by
Pierre Lindenbaum
160k • written 9 days ago by
Ronin
• 0
3
votes
2
replies
264
views
R: How to customize the legend order for a 3D scatter plot in plotly?
R
r
plotly
8 days ago by
SIV0625TriX
▴ 30
4
votes
3
replies
404
views
Single cluster spanning in different locations in UMAP in scRNAseq data
UMAP
scRNAseq
8 days ago by
sarahmanderni
▴ 100
2
votes
4
replies
354
views
Visualizing human genomic loci
Genome
visualization
3 days ago by
James
▴ 10
0
votes
4
replies
350
views
Biostrings extract read
R
fastq
Biostrings
9 days ago by
marco.barr
▴ 30
1
vote
2
replies
252
views
Detecting viruses in human rna seq data
RNA-Seq
Viruses
updated 9 days ago by
GenoMax
140k • written 9 days ago by
biochugs
• 0
0
votes
0
replies
149
views
Change orig.ident column in seurat meta.data to match cell barcode sample prefixes
seurat
9 days ago by
bgbs
• 0
1
vote
2
replies
276
views
Length by gene from salmon
salmon
RNA-seq
9 days ago by
marco.barr
▴ 30
5
votes
4
replies
351
views
change order of violin plots in ggplot2
R
ggplot2
violin-plots
updated 9 days ago by
Ram
43k • written 9 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
138
views
Motif analysis by HOMER
Homer
9 days ago by
daffodil
▴ 10
1
vote
2
replies
545
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
9 days ago by
e.r.zakiev
▴ 170
0
votes
5
replies
359
views
Error when trying to install R package 'scater'
scater
scRNA-Seq
updated 9 days ago by
Ram
43k • written 10 days ago by
Nitin
• 0
1
vote
4
replies
318
views
Long branch lengths, low bootstrap values and misalignments
mafft
muscle
iqtree
9 days ago by
samyu.senthil
▴ 10
5
votes
5
replies
347
views
Including reference genome in SNP-based phylogeny
phylogeny
VCF
WGS
8 days ago by
maxrwjones
▴ 60
2
votes
5
replies
386
views
How to add FORMAT/TAG = "." to all samples in a vcf file via bcftools?
vcf
bcftools
updated 9 days ago by
Pierre Lindenbaum
160k • written 10 days ago by
Марта
• 0
1
vote
1
reply
190
views
adding new assemblies to previously built practical haplotype graph (v2)
pangenome
phg_v2
plants
PHG
updated 10 days ago by
lcj34
▴ 410 • written 10 days ago by
b.contreras.moreira
▴ 70
0
votes
2
replies
355
views
Ribo and RNA seq analysis
RNA-seq
genomics
Ribo-seq
updated 10 days ago by
Jack Tierney
▴ 350 • written 5 weeks ago by
Manu Ayllon
• 0
0
votes
0
replies
133
views
DADA2 truncLen value
metabarcoding
phyloseq
DADA2
illumina
10 days ago by
Bioinfo
▴ 20
0
votes
1
reply
176
views
Resources regarding Proteomics (In-Silico)
proteomics
docking
protein
molecular-simulation
updated 9 days ago by
Ram
43k • written 10 days ago by
Saurabh
• 0
1
vote
0
replies
143
views
TensorQTL Mapping - permutation p values for all associations
permutation
TensorQTL
10 days ago by
Paula
▴ 10
0
votes
5
replies
408
views
Deeptools scale issue for plotHeatmap
deeptools
computeMatrix
plotHeatmap
6 days ago by
Learner
• 0
4
votes
1
reply
242
views
why there is an asterisk symbol at the end of each proteins sequences of fasta files in the Braker3 output?
gtf
breaker3
protein-seq
9 days ago by
mathavanbioinfo
▴ 80
1
vote
5
replies
410
views
Haddock 2.4
Protein
Docking
updated 9 days ago by
dthorbur
★ 1.7k • written 11 days ago by
Preeti
• 0
0
votes
2
replies
243
views
Beagle Phasing and Imputation
imputation
phasing
beagle
10 days ago by
Duarte Molha
▴ 240
1
vote
0
replies
110
views
ENVO Ontology to Annotate Plain Text
natural
language
NL
ontology
envo
10 days ago by
marie.harmel
▴ 10
2
votes
4
replies
349
views
Subsetting Seurat object based on list of cell barcodes
seurat
updated 10 days ago by
Ming Tommy Tang
★ 3.9k • written 10 days ago by
bgbs
• 0
832 results • Page
5 of 17
Recent Votes
F*up Night style events for Bioinformatics ? Comment if you're interested!
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Volume II
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
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Popular Question
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svlachavas
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Teacher
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160k
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Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Madelaine Gogol
5.3k
That sounds fun, and I've got some of these that I have told many people about (to keep them from making the same mistakes as me). I am pla…
Comment: Mapping ortholog human and mouse transcript
by
1769mkc
★ 1.2k
for hgnc and ensembl that can be done for transcript id for human to mouse ortholog its difficult to parse and map the exact version from g…
Comment: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of
by
Mensur Dlakic
★ 26k
Take it from someone who has hosted both a successful and a failed research topic: these deadlines are unrealistic. I am guessing you are p…
Answer: Tissue specific mRNA expression dataset in human and mouse
by
BioinfGuru
★ 1.6k
Awesome, years ago I wrote my thesis on the use of Tau to calculate tissue specificity, enjoy! The supplementary materials in the paper is…
Answer: Mapping ortholog human and mouse transcript
by
BioinfGuru
★ 1.6k
That error is on the server side, nothing to do with you, and is very common. Usually the fix is to try again in an hour, or to insert host…
Comment: Nanopore multisample variant calling
by
emilydolivo97
• 0
hello @colindaven , Did you find a suitable tool for this purpose please ? I'm dealing with fungal dataset
Comment: How do I get the gene annotations as a text file from a genebank file?
by
BioinfGuru
★ 1.6k
Can you upload or post a link to the genbank file please?
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
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