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120,728 results • Page
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CPTAC Data analysis
CPTAC
proteomics
just now by
jain72744
▴ 10
0
votes
0
replies
16
views
Seeking Advice on Data Processing for Differential Analysis in Bioinformatics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
9 minutes ago by
Riley J
• 0
0
votes
0
replies
15
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phylogenic analysis
biotechnology
biologist
Bioinformatics
computational
1 hour ago by
uttkarsh
• 0
78
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13
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41k
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10 follow
How Can I Get The Human Chromosome Centromere Position And Chromosome Length In Grch37/Hg19
position
ucsc
updated 1 hour ago by
Helix
▴ 20 • written 14.5 years ago by
Jdk
▴ 260
0
votes
3
replies
59
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 1 hour ago by
GenoMax
149k • written 3 hours ago by
omicon
• 0
0
votes
2
replies
35
views
Methylation cpg probes annotation
TCGA
methylation
cpg
annotation
1 hour ago by
jain72744
▴ 10
1
vote
2
replies
201
views
How to convert .ab1 to fastq
Fastq
updated 5 hours ago by
size_t
▴ 120 • written 1 day ago by
dr.suvarnakapale
• 0
1
vote
3
replies
78
views
Efficient Gene Prediction on Large Eukaryotic Genomes
tools
prediction
gene
updated 30 minutes ago by
colindaven
7.3k • written 5 hours ago by
Shuo
• 0
0
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0
replies
49
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
5 hours ago by
v.berriosfarias
▴ 140
0
votes
1
reply
115
views
PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Database
PPI
STRING
updated 7 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
bioinfo_enthusiast
• 0
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
0
replies
55
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
7 hours ago by
Jl
• 0
0
votes
1
reply
84
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 6 hours ago by
karl.stamm
4.1k • written 10 hours ago by
Megan
▴ 50
0
votes
1
reply
84
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
updated 10 hours ago by
LChart
4.9k • written 10 hours ago by
noodlejackson
▴ 40
0
votes
0
replies
60
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
11 hours ago by
emalekos
▴ 40
0
votes
1
reply
91
views
News:
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback
tool
updated 14 hours ago by
GenoMax
149k • written 16 hours ago by
genanalyzer24
• 0
0
votes
1
reply
96
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy
RNA-Seq
updated 14 hours ago by
ATpoint
87k • written 17 hours ago by
bioinfo1990
• 0
0
votes
0
replies
77
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
22 hours ago by
Mark
▴ 30
2
votes
1
reply
888
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
88
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
1 day ago by
1769mkc
★ 1.2k
0
votes
2
replies
229
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 1 day ago by
dsull
★ 7.3k • written 2 days ago by
brutonk
• 0
0
votes
0
replies
117
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
1 day ago by
Physalia-courses
★ 2.6k
1
vote
1
reply
203
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
409
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
124
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
12 hours ago by
Mllepnos
• 0
2
votes
0
replies
119
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
126
views
Can I combine segment results from Sequenza and cnvkit?
CNV
sequenza
cnvkit
2 days ago by
Ram
45k
2
votes
1
reply
240
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
updated 2 days ago by
grover.sandeep
▴ 20 • written 4 days ago by
s.may-wilson
▴ 50
0
votes
0
replies
130
views
News:
Multi-Omics Integration with Machine Learning — Online Course!
Machine-Learning
Multi-Omics
Depp-Learning
Data-Integration
BigData
2 days ago by
Physalia-courses
★ 2.6k
1
vote
2
replies
211
views
Alignment algorithm for DNA sequencing
sequencing
data
DNA
updated 2 days ago by
ATpoint
87k • written 2 days ago by
QX
▴ 70
0
votes
1
reply
193
views
RepeatMasker UCSC track
RepeatMasker
updated 2 days ago by
Michael
55k • written 2 days ago by
frarodmar17
• 0
0
votes
0
replies
145
views
rarefaction curve metagenomic reads show species saturation around 100 000 reads
metagenomics
rarefaction
kraken2
2 days ago by
rDNA
▴ 20
0
votes
4
replies
450
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 2 days ago by
jared.andrews07
★ 18k • written 5 days ago by
Pumla
• 0
9
votes
21
replies
7.7k
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
214
views
Looking up gene name from mRNA ID using biomaRt
R
mRNA
biomaRt
updated 2 days ago by
Ram
45k • written 3 days ago by
Khôi
• 0
0
votes
0
replies
162
views
Interpreting negative gap length in MUMMER4
mummer
translocation
3 days ago by
cedric.blais
▴ 20
0
votes
0
replies
147
views
Uncertainty about deepTools computeMatrix options for RNA modifications
deepTools
metagene
computeMatrix
3 days ago by
Kyle
• 0
0
votes
0
replies
142
views
News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
3 days ago by
soledad.esteban
• 0
6
votes
6
replies
556
views
Multiple factors in DESeq2
deseq2
3 days ago by
noodlejackson
▴ 40
10
votes
2
replies
310
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
299
views
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genomes
star
trinity
rnaseq
updated 3 days ago by
Ram
45k • written 3 days ago by
zizigolu
★ 4.3k
3
votes
7
replies
358
views
nanopore variant calling
pacBio
long-read
nanopore
updated 2 days ago by
colindaven
7.3k • written 3 days ago by
Meghan.T
• 0
0
votes
3
replies
319
views
enrichGo problem
enrichGo
updated 2 days ago by
Arup Ghosh
3.3k • written 3 days ago by
mimijane1664
• 0
1
vote
4
replies
315
views
Seeking Help for Reanalysis of Raw WES Data
WES
updated 3 days ago by
Jeremy Leipzig
23k • written 3 days ago by
lidia.manczak
• 0
1
vote
8
replies
329
views
Biscuit Alignment and Index failed - WGBS - Bisulfite analysis
BWA
Biscuit
Bisulfite
updated 3 days ago by
Ram
45k • written 3 days ago by
Palanikumar.Palanichamy
• 0
0
votes
3
replies
272
views
illumina: Adapter Confusion
ILLUMINA
ADAPTER
updated 3 days ago by
GenoMax
149k • written 4 days ago by
lingjun meng
▴ 20
2
votes
3
replies
291
views
Identifying primer sequences from raw FASTQ files
primers
2 days ago by
Chandini
• 0
2
votes
7
replies
1.4k
views
HTSlib threads when ingesting large bgzipped FASTA
htslib
samtools
bgzip
c
updated 3 days ago by
aw7
▴ 370 • written 20 months ago by
Oleksii
• 0
3
votes
3
replies
327
views
question for dowloading Protein fasta sequence by edirect using while
edirect
updated 4 days ago by
vkkodali_ncbi
★ 3.8k • written 4 days ago by
诗友
• 0
2
votes
2
replies
736
views
Validate RNAseq Models in Microarray Data?
microarray
rnaseq
coxlasso
fpkm
updated 3 days ago by
ATpoint
87k • written 2.7 years ago by
vitor
▴ 130
120,728 results • Page
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ggalign: alternative to ComplexHeatmap, a ggplot2 extension for complex heatmap and marginal plots.
Comment: Efficient Gene Prediction on Large Eukaryotic Genomes
Answer: Reasoning - Why is it invalid to compare ratios of TPMs?
Snakemake version 8.27.1 on LSF cluster
Minimal Quality Control Thresholds in Shotgun or Amplicon Metagenomics for non assembly based analysis
Metagenomics/amplicon sequencing: Most publicly available data already host removed sequences or no?
Guided genome assembly
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Comment: Efficient Gene Prediction on Large Eukaryotic Genomes
by
colindaven
7.3k
As others have said, 2 hours is nothing. Wait till you get to assembly or long read alignment. The quality of results is far more important…
Comment: Methylation cpg probes annotation
by
jain72744
▴ 10
So how to compare their differential expression to transcriptomics data
Comment: Annotations Tools
by
abebe1423
• 0
thank you, dear, I want to do, first merge the vcf file from 4 callers after that, I want to annotation it using annotation tools So I …
Answer: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
by
Helix
▴ 20
You can pre-process this file [http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/gap.txt.gz][1] and extract the centromeric regions f…
Comment: How to Process Multiple SRRs for the Same BioSample ?
by
GenoMax
149k
> I’m concerned about merging the FASTQ files due to potential batch effects. Would it be better to process everything separately? You cou…
Comment: Methylation cpg probes annotation
by
LChart
4.9k
Not all cpgs are within or proximal to genes.
Comment: How to Process Multiple SRRs for the Same BioSample ?
by
omicon
• 0
Hi, thank you! I’ve already read the paper and reviewed the metadata, but I couldn’t find any additional relevant information. Yes, there…
Answer: How to Process Multiple SRRs for the Same BioSample ?
by
GenoMax
149k
Looking at the metadata table for this project gives additional clues: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA528920&o=acc_s%3…
Comment: Efficient Gene Prediction on Large Eukaryotic Genomes
by
GenoMax
149k
> on a large eukaryotic genome dataset and > I found that it runs quite slowly, often taking up to two hours to process a single FASTA fi…
Comment: Efficient Gene Prediction on Large Eukaryotic Genomes
by
Mensur Dlakic
★ 29k
Not sure why we are discussing this. Is it more important to you to get these gene predictions right, or to save 20-50 hours? Unless you ha…
Answer: How to convert .ab1 to fastq
by
size_t
▴ 120
try this gui tool: https://technelysium.com.au/wp/chromas/
Comment: Is there too little variation to detect meaningful gene changes?
by
karl.stamm
4.1k
So there's no difference. Reasonable result. Triple check your protocol and sample handling, did they get mixed up? Did they get processed…
Answer: PPI Network Analysis of Virulence Genes in Morganella morganii Using STRING Data
by
Mensur Dlakic
★ 29k
The simplest way I can think of is to assign best BLAST matches to your proteins from an annotated *M. morganii* genome. Then transfer the …
Answer: How to make amazing UMAP to spatialPlot GIF
by
LChart
4.9k
Looks to me to be a sequence of intermediate linear interpolations. For each point you have coordinates (U1, U2) for the UMAP plot, (S1, S2…
Comment: Detecting Aneuploidy from Bulk RNA-Seq Data
by
ATpoint
87k
Not my field, but a) I would doubt that the highly uneven coverage of RNA-seq allows for inference like that other than plotting count dist…
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