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120,734 results • Page
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How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
elegans
Foldseek
C
Genes
Orthologs
Homologs
just now by
bioinformatics_rk
• 0
0
votes
3
replies
118
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 42 minutes ago by
swbarnes2
14k • written 18 hours ago by
Megan
▴ 50
0
votes
0
replies
13
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
50 minutes ago by
baibhu1234
▴ 20
0
votes
1
reply
97
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 57 minutes ago by
shelkmike
★ 1.5k • written 1 day ago by
Mark
▴ 30
0
votes
1
reply
66
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 1 hour ago by
shelkmike
★ 1.5k • written 6 hours ago by
Ariadna
▴ 20
0
votes
1
reply
77
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
updated 1 hour ago by
jared.andrews07
★ 18k • written 8 hours ago by
Riley J
• 0
0
votes
2
replies
41
views
Population genetics with mutect2 data
haplotypecaller
mutect2
just now by
slzr_
• 0
1
vote
2
replies
66
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 2 hours ago by
Watermelon
• 0 • written 3 hours ago by
gogeni5529
▴ 60
1
vote
2
replies
100
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 1 hour ago by
Ram
45k • written 9 hours ago by
uttkarsh
• 0
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
41
views
Chrom3D
chrom3d
interchromosomal
genome
model
6 hours ago by
desptsp
• 0
0
votes
1
reply
60
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
5 hours ago by
ZheFrench
▴ 590
1
vote
3
replies
99
views
CPTAC Data analysis
CPTAC
proteomics
updated 2 hours ago by
LauferVA
4.5k • written 8 hours ago by
jain72744
▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere
ucsc
updated 1 hour ago by
Ram
45k • written 14.5 years ago by
Jdk
▴ 260
0
votes
3
replies
112
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 10 hours ago by
GenoMax
150k • written 11 hours ago by
omicon
• 0
0
votes
3
replies
117
views
Methylation cpg probes annotation
annotation
methylation
cpg
TCGA
updated 6 hours ago by
GenoMax
150k • written 11 hours ago by
jain72744
▴ 10
1
vote
2
replies
225
views
How to convert .ab1 to fastq
Fastq
updated 13 hours ago by
size_t
▴ 120 • written 2 days ago by
dr.suvarnakapale
• 0
1
vote
3
replies
133
views
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 8 hours ago by
colindaven
7.3k • written 13 hours ago by
Shuo
• 0
0
votes
1
reply
92
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
updated 5 hours ago by
dthorbur
★ 2.9k • written 13 hours ago by
v.berriosfarias
▴ 140
0
votes
1
reply
132
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
updated 15 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
bioinfo_enthusiast
• 0
0
votes
1
reply
91
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
updated 5 hours ago by
dariober
15k • written 15 hours ago by
Jl
• 0
1
vote
2
replies
125
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
5 hours ago by
noodlejackson
▴ 40
0
votes
0
replies
74
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
19 hours ago by
emalekos
▴ 40
0
votes
1
reply
110
views
News:
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback
tool
updated 23 hours ago by
GenoMax
150k • written 1 day ago by
genanalyzer24
• 0
1
vote
1
reply
125
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy
RNA-Seq
updated 7 hours ago by
ATpoint
87k • written 1 day ago by
bioinfo1990
• 0
2
votes
1
reply
902
views
How to perform PPI network analysis in STRING for newly sequenced bacterial genome ?
Proteomics
cytoscape
network
STRING
updated 1 day ago by
bioinfo_enthusiast
• 0 • written 3.8 years ago by
Kumar
▴ 120
0
votes
0
replies
99
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
1 day ago by
1769mkc
★ 1.2k
0
votes
2
replies
247
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 2 days ago by
dsull
★ 7.3k • written 2 days ago by
brutonk
• 0
0
votes
0
replies
132
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
2 days ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
216
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
updated 2 days ago by
ATpoint
87k • written 2 days ago by
ATRX
★ 1.2k
0
votes
1
reply
423
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 2 days ago by
S
• 0 • written 4 weeks ago by
s
• 0
0
votes
0
replies
136
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
20 hours ago by
Mllepnos
• 0
2
votes
0
replies
129
views
Tool:
PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment
function
GO
goterms
geneontology
2 days ago by
geneontologyhelp
▴ 460
0
votes
0
replies
142
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
3 days ago by
Ram
45k
2
votes
1
reply
255
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
updated 3 days ago by
grover.sandeep
▴ 20 • written 4 days ago by
s.may-wilson
▴ 50
0
votes
0
replies
144
views
News:
Multi-Omics Integration with Machine Learning — Online Course!
Machine-Learning
Multi-Omics
Depp-Learning
Data-Integration
BigData
3 days ago by
Physalia-courses
★ 2.6k
3
votes
2
replies
237
views
Alignment algorithm for DNA sequencing
sequencing
data
DNA
updated 3 days ago by
ATpoint
87k • written 3 days ago by
QX
▴ 70
0
votes
1
reply
206
views
RepeatMasker UCSC track
RepeatMasker
updated 3 days ago by
Michael
55k • written 3 days ago by
frarodmar17
• 0
0
votes
0
replies
158
views
rarefaction curve metagenomic reads show species saturation around 100 000 reads
metagenomics
rarefaction
kraken2
3 days ago by
rDNA
▴ 20
0
votes
4
replies
471
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 3 days ago by
jared.andrews07
★ 18k • written 6 days ago by
Pumla
• 0
9
votes
21
replies
7.8k
views
12 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 3 days ago by
bagdevi.mishra
▴ 110 • written 6 months ago by
Martina
• 0
0
votes
2
replies
233
views
Looking up gene name from mRNA ID using biomaRt
R
mRNA
biomaRt
updated 3 days ago by
Ram
45k • written 3 days ago by
Khôi
• 0
0
votes
0
replies
176
views
Interpreting negative gap length in MUMMER4
mummer
translocation
3 days ago by
cedric.blais
▴ 20
0
votes
0
replies
158
views
Uncertainty about deepTools computeMatrix options for RNA modifications
deepTools
metagene
computeMatrix
3 days ago by
Kyle
• 0
0
votes
0
replies
153
views
News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
3 days ago by
soledad.esteban
• 0
6
votes
6
replies
569
views
Multiple factors in DESeq2
deseq2
3 days ago by
noodlejackson
▴ 40
10
votes
2
replies
319
views
Why do RNAseq reads align to non-gene regions of the bacterial genome?
RNAseq
transcription
updated 3 days ago by
i.sudbery
21k • written 4 days ago by
Texx
▴ 40
1
vote
1
reply
362
views
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genomes
star
trinity
rnaseq
updated 4 days ago by
Ram
45k • written 4 days ago by
zizigolu
★ 4.3k
3
votes
7
replies
377
views
nanopore variant calling
pacBio
long-read
nanopore
updated 3 days ago by
colindaven
7.3k • written 4 days ago by
Meghan.T
• 0
0
votes
3
replies
339
views
enrichGo problem
enrichGo
updated 3 days ago by
Arup Ghosh
3.3k • written 4 days ago by
mimijane1664
• 0
120,734 results • Page
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Recent Votes
Comment: ggplot of two data set with different colors
C: Extract Reads From A Bam File That Fall Within A Given Region
A: Extract Reads From A Bam File That Fall Within A Given Region
Extract Reads From A Bam File That Fall Within A Given Region
Answer: phylogenic analysis
Comment: CPTAC Data analysis
Comment: Help with rownames in DESeq2
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Recent Replies
Comment: Is there too little variation to detect meaningful gene changes?
by
swbarnes2
14k
I doubt your RNA quality is the issue. It's not likely that poor quality would cause reads to align to the wrong gene. Its far more likely …
Comment: Is there too little variation to detect meaningful gene changes?
by
Megan
▴ 50
The RIN values for these samples ranged around 6.0-7.0, which I think would suggest RNA degradation. From what I am aware of, I don't think…
Answer: Recommendations for Reference-guided de novo assembly assembly approaches or pip
by
shelkmike
★ 1.5k
You can do a de novo assembly and then scaffold the contigs using a reference by RagTag (https://github.com/malonge/RagTag). However, I per…
Answer: Per Base Sequence Content FastQC
by
shelkmike
★ 1.5k
The difference between (A or T) and (G or C) may reflect the GC composition of the genome. Thus, it is not indicative of some sequencing pr…
Answer: Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transc
by
jared.andrews07
★ 18k
What do you mean by "non-raw" data? You're correct in that grabbing arbitrary values on different scales and trying to mash them together i…
Comment: phylogenic analysis
by
Ram
45k
None of the tags you used are relevant to the question you asked - they broadly describe the entire field of bioinformatics. I've fixed it …
Answer: Population genetics with mutect2 data
by
LauferVA
4.5k
Hi @slzr_ In short, no. What I mean is, it’s generally not recommended to use Mutect2 calls directly for classical population genetics ana…
Comment: CPTAC Data analysis
by
LauferVA
4.5k
Please note also that there are also forums that directly relate to CPTAC (only), which may be more appropriate depending on the nature of …
Answer: ggplot of two data set with different colors
by
Watermelon
• 0
Try ggnewscale package, add new_scale_color() between the plots. Something like this should work ggplot() + geom_line(data = gr…
Comment: ggplot of two data set with different colors
by
Arup Ghosh
3.3k
You are trying to colour the same gene names with two different codes. Either make two subplots for the groups or change the shape of dots …
Comment: CPTAC Data analysis
by
jain72744
▴ 10
Considering your suggestion, I'd like to elaborate what I wish to find. I started with proteomics analysis form TCGA data obtaining the pro…
Comment: How to make amazing UMAP to spatialPlot GIF
by
noodlejackson
▴ 40
Thank you @LChart, wow that sounds like a very elegant solution! I've got the seurat currently in R. I'll export to python and give it a ba…
Comment: How to deal with missing annotations in RNASeq data?
by
dthorbur
★ 2.9k
What do you mean by "low characterized plant species"? How many gene predictions does it have? There are a few options I see: 1. If …
Answer: phylogenic analysis
by
dthorbur
★ 2.9k
This question is hard to answer without much context, but there are some generalisations that might be useful. Ultimately, the answer i…
Comment: How to identify 16s sequences from binning data(contigs)?
by
Laura
• 0
Hi @layne_sadler — were you able to resolve this issue? Also, if you ended up creating your own database using a more recent SILVA release,…
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