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576 results • Page
2 of 12
Sort: Rank
Rank
Views
Votes
Replies
0
votes
4
replies
367
views
What are recommended parameters for the local protein alignment ?
protein
alignment
3 days ago by
Alexander
▴ 70
0
votes
0
replies
130
views
microsatellite, SSR, using Galaxy
Galaxy
SSR
using
microsatellite
4 days ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
146
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue
padj
decoupleR
4 days ago by
OST
▴ 10
2
votes
3
replies
342
views
Low mapping percentage
mapping
STAR
RNAseq
3 days ago by
Sib
▴ 40
0
votes
0
replies
172
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
4 days ago by
Mark
• 0
0
votes
0
replies
160
views
busco id description
OrthoDB
BUSCO
updated 4 days ago by
Ram
39k • written 5 days ago by
angelina
• 0
0
votes
5
replies
390
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 4 days ago by
Joe
21k • written 5 days ago by
gunala.nikhil
• 0
0
votes
0
replies
164
views
NMDS plotting issue
NMDS
metagenomic
5 days ago by
arshad1292
▴ 90
0
votes
2
replies
239
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
1 day ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
142
views
IGV insertions
insertions
IGV
5 days ago by
christoph.schubart
• 0
1
vote
0
replies
155
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 4 days ago by
Ram
39k • written 5 days ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
149
views
jellyfish options
kmer
jellyfish
5 days ago by
Tele
• 0
0
votes
3
replies
227
views
hardfilter error
bam
recall
5 days ago by
bestone
▴ 10
0
votes
0
replies
124
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
5 days ago by
Omics data mining
▴ 220
0
votes
0
replies
125
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 5 days ago by
GenoMax
130k • written 5 days ago by
Dablax
• 0
1
vote
1
reply
600
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 5 days ago by
GenoMax
130k • written 5 days ago by
Mohd
▴ 20
0
votes
0
replies
117
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
5 days ago by
Alexandre
• 0
0
votes
1
reply
185
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 5 days ago by
raphael.B
▴ 360 • written 5 days ago by
sonsunjirachote
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
1
vote
2
replies
229
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 4 days ago by
thadjudkins2
• 0 • written 5 days ago by
herh
• 0
1
vote
0
replies
143
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
5 days ago by
abba647
▴ 10
4
votes
4
replies
294
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 5 days ago by
bioinfo
▴ 80
0
votes
1
reply
165
views
Merge different vcf files
vcf
updated 4 days ago by
Ram
39k • written 5 days ago by
caique.manochio
• 0
0
votes
4
replies
279
views
Identification of genes involved in my pathway
KEGG
keggGet
5 days ago by
smanzano250800
• 0
0
votes
8
replies
349
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 5 days ago by
GenoMax
130k • written 6 days ago by
Marta
• 0
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
2 days ago by
Maria17
▴ 20
1
vote
0
replies
97
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
6 days ago by
Jonathan Lefebre
▴ 70
0
votes
3
replies
180
views
DEGseq for multiple samples
DEGseq
DEG
updated 6 days ago by
Ram
39k • written 6 days ago by
ALOUSH ALI
• 0
0
votes
0
replies
80
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 6 days ago by
Ram
39k • written 6 days ago by
Rishabh Jha
• 0
1
vote
3
replies
210
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 6 days ago by
GenoMax
130k • written 6 days ago by
NikhilP
▴ 20
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 23 hours ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
0
replies
106
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
6 days ago by
mbk0asis
▴ 670
0
votes
0
replies
303
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
106
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 6 days ago by
Ram
39k • written 6 days ago by
Mah
• 0
1
vote
3
replies
221
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 6 days ago by
GenoMax
130k • written 6 days ago by
mls
• 0
0
votes
0
replies
109
views
snpEff error. No CDS checked
snpEff
gtf
WES
6 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
111
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
6 days ago by
Maddie
• 0
1
vote
2
replies
209
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
5 days ago by
rheab1230
▴ 140
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 6 days ago by
Ram
39k • written 6 days ago by
miguellarrazlopezdenovales
• 0
1
vote
0
replies
107
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
6 days ago by
fr
▴ 200
0
votes
2
replies
175
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 6 days ago by
rpolicastro
12k • written 7 days ago by
Pac314
▴ 10
0
votes
2
replies
167
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 days ago by
survive
• 0
1
vote
1
reply
130
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 7 days ago by
GenoMax
130k • written 7 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
80
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
7 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
190
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 7 days ago by
herh
• 0
0
votes
0
replies
75
views
1000G reference panel for LD clumping
LD
7 days ago by
en_keser
• 0
0
votes
0
replies
85
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
7 days ago by
saladi
▴ 30
0
votes
2
replies
612
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 7 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
7
replies
579
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 7 days ago by
Vincent Laufer
★ 2.9k • written 11 days ago by
Camilo Andres
▴ 30
576 results • Page
2 of 12
Recent Votes
Comment: ChatGPT optimized for bioinformatics questions
Answer: counts matrix should be numeric, currently it has mode: character when using a c
ChatGPT optimized for bioinformatics questions
Answer: Limma returned only positive logFC values
Answer: Limma returned only positive logFC values
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
Comment: ChatGPT optimized for bioinformatics questions
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Comment: Is PanCan data microarray or rna-seq
by
solarchan7
• 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c
by
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4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome
by
Basti
★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
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gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
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72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
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130k
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4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
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Was a tool ever found for this? I am curious.
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I never used it myself so far, but I would proably look into https://bioconductor.org/packages/devel/bioc/vignettes/nullranges/inst/doc/nul…
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Since you have kept the bot openly accessible (at least for now) this is great. People can try it out and hopefully provide feedback. I tri…
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if you are doing these steps then the `R` version should be `4.1.1`. Are you sure there weren't any errors during the install of `r-base=4.…
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Please follow this sequence of steps and show us the outputs: ``` # Start from a fresh terminal with no conda environment active: which -a…
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Happy to help!
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Thanks for the info. I called the --compliant and later removed the Ec_number of hypothetical protein as mentioned by NCBI table2asn guidel…
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