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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 ▴ 150 • written 9 hours ago by • 0
4
votes
3
replies
122
views
Hierarchical Clustering of GO terms
Clustering GO similarity Ontology
updated 1 day ago by 72k • written 1 day ago by ▴ 160
0
votes
0
replies
81
views
News: 3-day ONLINE TRAINING - NEXTFLOW
pipeline programming workflow cloud clustering
updated 13 days ago by 99k • written 13 days ago by ★ 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 5.3k • written 15 days ago by • 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 ★ 10k • written 17 days ago by • 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 20 • written 9 weeks ago by • 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 ▴ 130 • written 6 weeks ago by • 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 ★ 10k • written 6 weeks ago by ▴ 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 ★ 2.7k • written 8 weeks ago by ▴ 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 ▴ 440 • written 4 months ago by ▴ 70
2
votes
11
replies
6.9k
views
7 follow
CD-HIT Clustering output
CD-HIT Clustering
updated 4 months ago by ▴ 70 • written 6.7 years ago by • 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 19k • written 5 months ago by • 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 ▴ 720 • written 7 months ago by ▴ 200
1
vote
2
replies
213
views
optimal number of clusters from distance matrix input
clustering R
updated 5 months ago by 72k • written 5 months ago by ▴ 90
0
votes
4
replies
307
views
Interpretation of two PCA plots
RNA-Seq pca clustering
updated 5 months ago by 9.7k • written 5 months ago by ▴ 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 6.9k • written 5 months ago by ▴ 40
0
votes
2
replies
341
views
Visualise CD-HIT clusters?
clustering data visualisation CD-HIT
updated 6 months ago by 20 • written 8 months ago by ▴ 60
2
votes
1
reply
310
views
Scaling RNA-Seq data before clustering?
RNA-Seq Clustering Hierarchical clustering Scaling
updated 6 months ago by 47k • written 6 months ago by • 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 ▴ 100 • written 13 months ago by ▴ 280
6
votes
6
replies
3.0k
views
Clustering of genes using FPKM
RNA-Seq clustering FPKM R bioconductor
updated 6 months ago by ★ 1.3k • written 6.3 years ago by ★ 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 • 0 • written 11 months ago by ▴ 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 ▴ 20 • written 17 months ago by ▴ 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 ★ 2.1k • written 7 months ago by ★ 2.0k
0
votes
1
reply
224
views
Export CLANS clusters in separate multifasta files
CLANS clustering FASTA
updated 8 months ago by 20 • written 9 months ago by ▴ 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 24k • written 8 months ago by ▴ 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 72k • written 9 months ago by • 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 20 • written 9.3 years ago by ▴ 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 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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