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439 results • Page
1 of 9
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Filtering for tag:
clustering
•
reset
3
votes
5
replies
115
views
RNAseq data analysis of pooled data
DESeq2
mapping
featurecounts
clustering
RNA-Seq
updated 2 hours ago by
ponganta
▴ 150 • written 9 hours ago by
luffy
• 0
4
votes
3
replies
122
views
Hierarchical Clustering of GO terms
Clustering
GO
similarity
Ontology
updated 1 day ago by
Kevin Blighe
72k • written 1 day ago by
The
▴ 160
0
votes
0
replies
81
views
News:
3-day ONLINE TRAINING - NEXTFLOW
pipeline
programming
workflow
cloud
clustering
updated 13 days ago by
GenoMax
99k • written 13 days ago by
carlopecoraro2
★ 2.0k
3
votes
2
replies
259
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering
pathways
complexheatmap
pheatmap
12 days ago by
Ridha
▴ 20
0
votes
7
replies
383
views
Cannot resize rowlabels in aheatmap
clustering
aheatmap
R
updated 12 days ago by
Santosh Anand
5.3k • written 15 days ago by
shaden
• 0
0
votes
0
replies
68
views
how to define open-pangenome?
python
fasta
genome
dna
clustering
14 days ago by
Kumar
▴ 50
5
votes
4
replies
314
views
Interpretation of Principal component analysis
clustering
updated 14 days ago by
Mensur Dlakic
★ 10k • written 17 days ago by
xqyn
• 0
1
vote
2
replies
204
views
Clustering two different RNA-seq timeseries results to identify shared/opposite gene patterns?
RNA-seq
trajectories
timeseries
clustering
2 days ago by
kelen
▴ 160
0
votes
0
replies
98
views
Identify cell type from bulk RNA sequencing data
sequencing
type
clustering
r
18 days ago by
minoo
• 0
0
votes
0
replies
159
views
Does anyone succeded clustering TCGA data?
RNA-Seq
TCGA
clustering
updated 5 weeks ago by
Biostar
20 • written 9 weeks ago by
Omar Mohamed
• 0
1
vote
1
reply
120
views
determine the robustness of single-cell clusters
clustering
RNA-Seq
rna-seq
R
Seurat
updated 6 weeks ago by
fracarb8
▴ 130 • written 6 weeks ago by
Maria17
• 0
0
votes
0
replies
98
views
Cluster Stability Assesment
rna-seq
Seurat
clustering
R
6 weeks ago by
Maria17
• 0
3
votes
5
replies
117
views
Clustering sequences with low identity
clustering
sequences
updated 6 weeks ago by
Mensur Dlakic
★ 10k • written 6 weeks ago by
agata88
▴ 810
1
vote
3
replies
153
views
How to run nucmer without reference? (viruses metagenomics)
assembly
clustering
metagenomics
virus
nucmer
updated 7 weeks ago by
colindaven
★ 2.7k • written 8 weeks ago by
Arsenal
▴ 30
3
votes
5
replies
258
views
Is my WGCNA soft threshold (power) too low?
wgcna
RNA-Seq
clustering
network
8 weeks ago by
jfaberha
• 0
0
votes
0
replies
139
views
Using ATACseq CPM for clustering samples
ATAC-seq
normalization
clustering
11 weeks ago by
barati
• 0
6
votes
5
replies
186
views
CD-HIT: representative sequence vs consensus sequence
CD-HIT
clustering
11 weeks ago by
rob_DNA
▴ 10
0
votes
0
replies
162
views
Cluster sequences in a network by their editing distance - in R
R
network analysis
clustering
editing distance
3 months ago by
fendermannn
• 0
0
votes
1
reply
201
views
How to select the number of clusters once I have the HCL (average linkeage) tree
hierarchical
clustering
gene
co-expression
3 months ago by
sofiablancoglez
• 0
1
vote
1
reply
509
views
Which tool for clustering (sub-networking) of protein-protein interaction networks based on the Gene Ontology Biological Process of proteins?
cytoscape
clustering
Gene Ontology
sub-network
updated 4 months ago by
scooter
▴ 440 • written 4 months ago by
Farah
▴ 70
2
votes
11
replies
6.9k
views
7 follow
CD-HIT Clustering output
CD-HIT
Clustering
updated 4 months ago by
bagdevi.mishra
▴ 70 • written 6.7 years ago by
BSP
• 0
0
votes
0
replies
237
views
Analyze RPPA cancer data in R for clustering patients and differential protein expression
RPPA
RPPanalyzer
R
clustering
DE
4 months ago by
svlachavas
▴ 730
3
votes
3
replies
200
views
Clustering similiar genes from many genomes
Python
genome
pangenomics
clustering
updated 4 months ago by
Joe
19k • written 5 months ago by
anabaena
• 0
0
votes
4
replies
210
views
identification of rare cell population in Sc-RNA sequencing
rna-seq
R
clustering
rare population
seurat
5 months ago by
Maria17
• 0
1
vote
2
replies
230
views
How to do unsupervised clustering of RNA-Seq data
RNA-Seq
clustering
next-gen
5 months ago by
Manoj
▴ 90
2
votes
1
reply
327
views
Correlating metadata with expression based k-means cluster (in R)
R
k-means
clustering
updated 5 months ago by
Papyrus
▴ 720 • written 7 months ago by
Sebastian Hesse
▴ 200
1
vote
2
replies
213
views
optimal number of clusters from distance matrix input
clustering
R
updated 5 months ago by
Kevin Blighe
72k • written 5 months ago by
lagartija
▴ 90
0
votes
4
replies
307
views
Interpretation of two PCA plots
RNA-Seq
pca
clustering
updated 5 months ago by
swbarnes2
9.7k • written 5 months ago by
newbie
▴ 90
2
votes
10
replies
254
views
How to identify which genes are responsible for the different cluster without PCA
R
hclust
clustering
bulkRNAseq
updated 5 months ago by
Friederike
6.9k • written 5 months ago by
camillab.
▴ 40
0
votes
2
replies
341
views
Visualise CD-HIT clusters?
clustering
data visualisation
CD-HIT
updated 6 months ago by
Biostar
20 • written 8 months ago by
jamie.pike
▴ 60
2
votes
1
reply
310
views
Scaling RNA-Seq data before clustering?
RNA-Seq
Clustering
Hierarchical clustering
Scaling
updated 6 months ago by
ATpoint
47k • written 6 months ago by
im
• 0
0
votes
3
replies
235
views
Differencial expression analysis between groups determined by two variables
expression
microarray
clustering
6 months ago by
jeni
▴ 50
8
votes
11
replies
2.3k
views
How many PCs should be considered for downstream analyses?
scRNAseq
PCA
UMAP
Clustering
RNAseq
updated 6 months ago by
Eugene A
▴ 100 • written 13 months ago by
bioinforesearchquestions
▴ 280
6
votes
6
replies
3.0k
views
Clustering of genes using FPKM
RNA-Seq
clustering
FPKM
R
bioconductor
updated 6 months ago by
Hamid Ghaedi
★ 1.3k • written 6.3 years ago by
Ron
★ 1.0k
1
vote
7
replies
918
views
Result of scanpy tools rank_genes_groups
gene
scanpy
seurat
rank_gene_groups
clustering
updated 7 months ago by
zf.math2013
• 0 • written 11 months ago by
el24
▴ 20
2
votes
5
replies
605
views
Best package to cluster a single cell dataset using marker gene lists retrieved from elsewhere?
RNA-Seq
single cell sequencing
clustering
updated 7 months ago by
paria.alipour
▴ 20 • written 17 months ago by
A248
▴ 10
0
votes
0
replies
193
views
individual-level allele frequencies
allele frequencies
clustering
plink
7 months ago by
anamaria
▴ 140
5
votes
3
replies
406
views
Which is the proper RNA-seq count table transformation to perform hierarchial clustering analysis?
RNA-Seq
stats
clustering
updated 7 months ago by
benformatics
★ 2.1k • written 7 months ago by
antonioggsousa
★ 2.0k
0
votes
1
reply
224
views
Export CLANS clusters in separate multifasta files
CLANS
clustering
FASTA
updated 8 months ago by
Biostar
20 • written 9 months ago by
hazirliver
▴ 10
2
votes
2
replies
306
views
error in hcluster although there is no NA/NAN/infinite
R
Heatmap
clustering
updated 8 months ago by
Jean-Karim Heriche
24k • written 8 months ago by
Kai_Qi
▴ 100
0
votes
1
reply
643
views
Converting mouse Ensembl ID's to gene names in a data frame
RNA-Seq
R
biomart
pheatmap
clustering
updated 9 months ago by
Kevin Blighe
72k • written 9 months ago by
lmck0705
• 0
0
votes
0
replies
172
views
Clustering with Sleipnir
microarray
clustering
gtr
9 months ago by
crouch.k
▴ 30
4
votes
2
replies
3.8k
views
Which Method Is The Best Dissimilarity Measurement For Hierarchical Clustering Of Dna Methylation Data
dna
methylation
clustering
updated 9 months ago by
Biostar
20 • written 9.3 years ago by
Gangcai
▴ 230
2
votes
11
replies
298
views
Sequence clustering tool that can break sequences?
clustering
10 months ago by
liorglic
▴ 340
0
votes
0
replies
434
views
R package for clustering time-series gene expression data with replicates in any time points (states)
time-serise
clustering
R
10 months ago by
maleknias
▴ 40
0
votes
4
replies
341
views
GSVA score and 1-Pearson correlation results do not harmonize
R
GSVA
Clustering
10 months ago by
aaragak1
▴ 40
2
votes
5
replies
395
views
Error while using ComplexHeatmap
R
data.frame
ComplexHeatmap
heatmap
clustering
10 months ago by
mohammedtoufiq91
▴ 110
3
votes
2
replies
257
views
How to check if there is an association between clustering output (groups) and phenotypic variables (gender, disease stage)
Clustering
Association
phenotype
statistics
10 months ago by
Bioinformatist Newbie
▴ 250
18
votes
1
reply
2.1k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
complexheatmap
clustering
arthritis
pam
Tutorial
10 months ago by
Kevin Blighe
72k
4
votes
9
replies
799
views
plotHeatmap for clustering samples
deeptools
plotHeatmap
computeMatrix
clustering
10 months ago by
jamzaleg84
▴ 50
439 results • Page
1 of 9
Recent Votes
C: What is difference between bulk RNAseq and mRNAseq?
Answer: Taxonomy assignment of viral RNA
Answer: RNAseq data analysis of pooled data
Comment: RNAseq data analysis of pooled data
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
A: How to select lines (filter) in vcf files that have same genotypes for all the s
A: How to select lines (filter) in vcf files that have same genotypes for all the s
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Recent Awards •
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Teacher
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Jean-Karim Heriche
24k
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biobiu
▴ 120
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Recent Replies
Comment: Taxonomy assignment of viral RNA
by
biobiu
▴ 120
Thanks! As for the blast option- (1) so do you suggest to just blast the contig against a db of viral RNAs? and (2) is there a comprehensiv…
Comment: Finding how many times a nucleotide appear in the same position
by
cpad0112
15k
#!/usr/bin/env python3 sequences = ["GAGGTAAACTCTG", "TCCGTAAGTTTTC", "CAGGTTGGAACTC", "ACAGTCAGTTCAC", "TAGGTCATTACAG", "TAGG…
Comment: Testing independence between 5' and 3' terminal sequences in a DNA database
by
Anand Rao
▴ 350
Thanks for your reply. Yes, I think I could have explained my problem much better, but rather than change my original post, I will add some…
Answer: Finding how many times a nucleotide appear in the same position
by
Dunois
▴ 600
Here's a little `python` function you can work off of: def count_quer_at_pos_in_seq(seqs, quer = "A"): #Initialize a list…
Comment: Using outgroup in gene family dendograms
by
Rogerio Ribeiro
▴ 50
Thank for the fast reponse. The ABC family is not the best example for this question indeed. The objective of my work is to find genes resp…
Answer: Taxonomy assignment of viral RNA
by
Zhilong Jia
★ 1.7k
1. Blast directly 2. [IDSeq][1], can get viral contigs and their annotation directly. [IDSeq : An open-source cloud-based pipeline and…
Comment: Finding how many times a nucleotide appear in the same position
by
hugo.avila
▴ 180
Hi, It is not a norm but it is a good practice to post an attempted resolution first and then other members try to correct it or suggest an…
Comment: What Do You Waste Your Time On
by
ponganta
▴ 150
Aye to the rushed analyses and the last-minute documentation. Horrible, but somehow it happens all the time.
Answer: What Do You Waste Your Time On
by
ponganta
▴ 150
Reinventing the wheel. Like, all the time. Why use clusterProfiler with an up-to-date GO-annotation, when you can just write your own clien…
Comment: RNAseq data analysis of pooled data
by
ponganta
▴ 150
By "pooled" data, do you mean data from tissue-specific bulk-RNAseq? Or did you pool single cell (SC) RNAseq-libraries?
Comment: RNAseq data analysis of pooled data
by
Dunois
▴ 600
What exactly do you mean by "pooled" data?
Answer: RNAseq data analysis of pooled data
by
grant.hovhannisyan
★ 2.1k
I made a tutorial last year for University students on this topic https://www.loom.com/share/a55c1dedb8e64e7cac47f6595b751de7. Let me know …
Comment: RNAseq data analysis of pooled data
by
luffy
• 0
@dunois Thank you for the tutorial, what are your thoughts for approach for pooled data? should i follow the documentation/the tutorial or …
Comment: How to extract only the specific fasta sequences by matching the ID's to a diff
by
pinn
▴ 90
In my case, it doesn't work. parallel --verbose 'echo "TRINITY_{}" > test__.txt | seqtk subseq /home/sunn/data/softwares/evaluation/Tr…
Comment: How to extract all columns of CSQ using split-vep plugin of bcftools?
by
Pierre Lindenbaum
135k
> extract all of them as table using is this plugin able to convert vcf to a tabular format ?
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