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116,591 results • Page
1 of 2332
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0
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74
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Network Alignment
plugin
Cytoscape
CytoMCS
updated 25 minutes ago by
Scooter
▴ 280 • written 20 hours ago by
Akash D
▴ 40
2
votes
4
replies
2.3k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 47 minutes ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
0
votes
0
replies
12
views
PCA plot
DESeq2
PCAplot
1 hour ago by
Aaliya
▴ 10
0
votes
0
replies
8
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
1 hour ago by
Ming Tommy Tang
★ 3.9k
0
votes
3
replies
214
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 2 hours ago by
Kevin Blighe
87k • written 1 day ago by
qudrat.nii
▴ 10
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 2 hours ago by
evawillms183
• 0 • written 8.3 years ago by
andrepleao
• 0
0
votes
0
replies
41
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
3 hours ago by
4fzcgueyp5
• 0
2
votes
3
replies
197
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
emmanouil.a
▴ 120
0
votes
1
reply
89
views
Annovar using R package
Annovar
gnomAD
R
updated 6 hours ago by
Pierre Lindenbaum
161k • written 8 hours ago by
DKA
▴ 40
0
votes
2
replies
122
views
Creating Synthetic Sequences for a ML Model
DNA
ML
updated 6 hours ago by
Mensur Dlakic
★ 27k • written 10 hours ago by
biochugs
• 0
3
votes
7
replies
322
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
1 hour ago by
Aaliya
▴ 10
0
votes
6
replies
617
views
Adding CB tag to bam file
samtools
bam
updated 8 hours ago by
swbarnes2
14k • written 6 days ago by
Maria
• 0
1
vote
10
replies
837
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
9 hours ago by
DKA
▴ 40
0
votes
0
replies
53
views
Finding orthologs between genome error
OMA
OMAbrowser
11 hours ago by
hemantcnaik
• 0
0
votes
2
replies
737
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 12 hours ago by
barslmn
★ 2.1k • written 2.8 years ago by
jhy
▴ 10
0
votes
3
replies
149
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 13 hours ago by
GenoMax
141k • written 14 hours ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
70
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 9 hours ago by
Ram
43k • written 14 hours ago by
glaciya2018
• 0
0
votes
0
replies
58
views
News:
8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling
DNAseq
illumina
RNAseq
transcriptomics
14 hours ago by
David Langenberger
11k
0
votes
0
replies
108
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
14 hours ago by
pramach1
▴ 40
0
votes
14
replies
3.4k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 15 hours ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
0
votes
1
reply
98
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 13 hours ago by
Sofia
• 0 • written 17 hours ago by
mawigoj318
• 0
0
votes
0
replies
80
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
19 hours ago by
salias
• 0
4
votes
5
replies
269
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 11 hours ago by
swbarnes2
14k • written 23 hours ago by
VITALA
• 0
0
votes
2
replies
143
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 9 hours ago by
Ram
43k • written 19 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
72
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 9 hours ago by
Ram
43k • written 19 hours ago by
newuser2024
• 0
0
votes
1
reply
110
views
alignment result
RNA-seq
samtools
hisat2
updated 9 hours ago by
Ram
43k • written 20 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
69
views
News:
hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models
GLM
R
updated 9 hours ago by
Ram
43k • written 21 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
63
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 9 hours ago by
Ram
43k • written 22 hours ago by
Jeyong
• 0
0
votes
2
replies
174
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
15 hours ago by
mropri
▴ 150
2
votes
2
replies
158
views
HaplotypeCaller - only SNPs
HaplotypeCaller
GATK
updated 1 day ago by
analyst
▴ 30 • written 1 day ago by
lorena9132
• 0
0
votes
0
replies
77
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
7
votes
2
replies
225
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
1
reply
167
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
Istvan Albert
100k • written 2 days ago by
Abeer
• 0
0
votes
4
replies
247
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
dxj294
• 0
0
votes
1
reply
115
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
198
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 9 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
1
reply
174
views
Seurat merge and batch correction
Seurat
updated 1 day ago by
Ram
43k • written 2 days ago by
sooni
▴ 20
1
vote
1
reply
144
views
Herald:
The Biostar Herald for Tuesday, April 23, 2024
herald
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Biostar
2.7k
1
vote
1
reply
119
views
Including plasmid in transcriptome assemblies
Bacteria
BOWTIE2
Transcriptomics
STAR
updated 1 day ago by
GenoMax
141k • written 1 day ago by
heelpPlease
• 0
2
votes
9
replies
789
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
357
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
128
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
3
votes
3
replies
191
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Estevão
• 0
0
votes
3
replies
210
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
updated 1 day ago by
Istvan Albert
100k • written 1 day ago by
Dylan
• 0
1
vote
4
replies
214
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 11 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
4
votes
11
replies
472
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 1 day ago by
LauferVA
4.2k • written 2 days ago by
dominickd
• 0
3
votes
13
replies
627
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 12 hours ago by
bk11
★ 2.3k • written 7 weeks ago by
Sofia
• 0
0
votes
0
replies
84
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
3
votes
0
replies
106
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
116,591 results • Page
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Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
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camillab.
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Recent Replies
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
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