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121,174 results • Page
1 of 2424
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1
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120
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Alternatives to WGCNA
WGCNA
updated 7 hours ago by
LChart
4.9k • written 19 hours ago by
Poorvi
▴ 10
2
votes
2
replies
141
views
RNA-seq analysis
Htseq-count
HiSat2
featurecounts
STAR
updated 10 hours ago by
Gordon Smyth
★ 8.0k • written 12 hours ago by
SEJAL
• 0
1
vote
2
replies
1.1k
views
Liquid Biopsy datasets
RNA-Seq
next-gen
liquid biopsy
miRNA
cDNA
updated 10 hours ago by
ehaag
▴ 20 • written 4.7 years ago by
pacocp
• 0
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 16 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
4
replies
961
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 10 hours ago by
ehaag
▴ 20 • written 10 months ago by
jimmysibandah
• 0
2
votes
3
replies
931
views
Metagenomics mock datasets
metagenomics
updated 10 hours ago by
ehaag
▴ 20 • written 16 months ago by
enuhblaise
• 0
0
votes
0
replies
58
views
GSEA and Cytoscape Enrichment maps
Cytoscape
RNA-seq
GSEA
12 hours ago by
kdca
• 0
0
votes
0
replies
88
views
News:
NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
NCBI
codeathon
genomics
13 hours ago by
MirianT_NCBI
▴ 770
1
vote
1
reply
126
views
Using structure prediction approaches to predict interaction between two proteins
protein
prediction
structure
updated 13 hours ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Daniel
▴ 30
0
votes
2
replies
117
views
How to visualize Combat-seq corrected counts
batch-correction
combat-seq
updated 8 hours ago by
cfos4698
★ 1.1k • written 14 hours ago by
ybw8gh
• 0
0
votes
2
replies
282
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 15 hours ago by
i.sudbery
21k • written 4 days ago by
sardius
• 0
2
votes
2
replies
117
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
14 hours ago by
1769mkc
★ 1.3k
0
votes
1
reply
157
views
Umbrella pathways in KEGG
KEGG
R
updated 18 hours ago by
Arup Ghosh
3.3k • written 1 day ago by
Arindam Ghosh
▴ 540
0
votes
2
replies
115
views
Peptide protein dynamics
Pepdide
updated 16 hours ago by
lieven.sterck
15k • written 18 hours ago by
venkatramananspd
• 0
2
votes
4
replies
169
views
variant calling chromosome-wise from WGS data
wgs
3 hours ago by
analyst
▴ 60
5
votes
5
replies
205
views
Design matrix with uneven patient representation across stages
RNA-seq
design-matrix
limma
18 hours ago by
Lucas
• 0
1
vote
2
replies
150
views
Forum:
The best LLM or any tool to generate legal regex expression string for specific usage?
regex
awk
sed
commands
linux
updated 21 hours ago by
GenoMax
151k • written 23 hours ago by
JustinZhang
▴ 140
0
votes
0
replies
69
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
1 day ago by
gulin
• 0
2
votes
6
replies
2.0k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 18 hours ago by
Arup Ghosh
3.3k • written 14 months ago by
michael.flower.14
▴ 200
0
votes
0
replies
77
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
1 day ago by
debitboro
▴ 270
3
votes
7
replies
275
views
Heatmap of a transformed deseq object with pheatmap
deseq2
pheatmap
updated 41 minutes ago by
SamGG
▴ 130 • written 1 day ago by
caroline.zanchi
• 0
5
votes
10
replies
2.7k
views
Minimap2 error in Flye de novo assembly
Flye
Minimap2
1 day ago by
Nilo
▴ 10
0
votes
0
replies
90
views
How to find hormone related proteins from a list of gene/proteins
R
updated 13 hours ago by
Ram
45k • written 1 day ago by
WUSCHEL
▴ 860
0
votes
0
replies
101
views
mtDNA variants from WGS data
mitogenome
WGS
updated 12 hours ago by
Ram
45k • written 1 day ago by
wonde2000
• 0
0
votes
1
reply
131
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF
LiftoverVcf
Merge
updated 1 day ago by
Giulio Genovese
▴ 630 • written 1 day ago by
JourneyToAbyss
▴ 240
0
votes
0
replies
95
views
Writing genepop from genind
R
genepop
genind
graph4lg
stacks
1 day ago by
eaabbott0
• 0
3
votes
4
replies
2.0k
views
Remove all entries with duplicate names from fastq file?
fastq
illumina
duplicate
updated 1 day ago by
Charles-Alexandre Roy
▴ 50 • written 3.9 years ago by
wormball
▴ 10
1
vote
1
reply
133
views
Copy Number Variants with CNVKit
CVNs
Somatic_variant
Recommendations
CNVKit
updated 1 day ago by
GenoMax
151k • written 1 day ago by
AIMAR
• 0
0
votes
0
replies
106
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
1 day ago by
aj
• 0
0
votes
0
replies
109
views
TEtranscripts analysis
TEtranscripts
1 day ago by
frarodmar17
• 0
0
votes
0
replies
112
views
CVNkit call commande
CVNs
CNVKit
Somatic_variant
1 day ago by
AIMAR
• 0
0
votes
3
replies
196
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
updated 18 hours ago by
marco.barr
▴ 170 • written 1 day ago by
n_navy
• 0
0
votes
1
reply
169
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq
DEGs
updated 23 hours ago by
manaswwm
▴ 570 • written 1 day ago by
noodlejackson
▴ 40
2
votes
3
replies
429
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 1 day ago by
GenoMax
151k • written 12 days ago by
Ambuj
• 0
0
votes
0
replies
110
views
News:
Online course: Introduction to R and Bioconductor
R
Bioconductor
Genomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
110
views
IM-fusion data analysis
IM-fusion
1 day ago by
frarodmar17
• 0
0
votes
4
replies
245
views
error in reading codelink data
readcodelinkset
5 hours ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
180
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 2 days ago by
Aspire
▴ 380 • written 2 days ago by
stalo.lili
• 0
7
votes
5
replies
632
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 1 day ago by
cmdcolin
★ 4.2k • written 16 days ago by
Pierre Lindenbaum
166k
8
votes
6
replies
3.3k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 1 day ago by
GenoMax
151k • written 12.1 years ago by
Mary
11k
1
vote
1
reply
252
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data
Breast-Cancer
TCGA
updated 2 days ago by
Zhenyu Zhang
★ 1.3k • written 4 days ago by
BhagyashreeWaghale
• 0
0
votes
2
replies
285
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 2 days ago by
GenoMax
151k • written 3 days ago by
bioinfo
▴ 150
0
votes
0
replies
170
views
Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV
purity
genome
ploidy
3 days ago by
ting
• 0
9
votes
8
replies
698
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow
workflow
pipeline
3 days ago by
neng
▴ 40
0
votes
1
reply
234
views
What to choose as background in statistic test genetics
test
expression
gene
statistic
updated 3 days ago by
Dunois
★ 2.9k • written 3 days ago by
adigershon8897
• 0
5
votes
4
replies
472
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
updated 3 days ago by
Gordon Smyth
★ 8.0k • written 6 days ago by
n_navy
• 0
0
votes
0
replies
372
views
Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics
genetic-variation
epistasis
snp
gnomad
4 days ago by
SonicSoal
• 0
0
votes
0
replies
184
views
Rare variants association analysis (using WGS)
variant
GWAS
rare
WGS
4 days ago by
SeoG
• 0
0
votes
0
replies
195
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat
segmentation
anndata
visiumhd
updated 4 days ago by
GenoMax
151k • written 4 days ago by
npont
• 0
0
votes
0
replies
202
views
News:
Online course -Reproducibility in Bioinformatics - July 7–9
Singularity
Git
Docker
Snakemake
Nextflow
4 days ago by
Physalia-courses
★ 2.6k
121,174 results • Page
1 of 2424
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Answer: Single Cell Density Scatter Plot with Seruat
Answer: RNA-seq analysis
Answer: RNA-seq analysis
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Comment: Heatmap of a transformed deseq object with pheatmap
by
SamGG
▴ 130
`rownames(expr_matrix) <- paste(genes,"-",gene_names)` will avoid to pass labels_row and allows to keep custom names synchronized with the …
Comment: variant calling chromosome-wise from WGS data
by
analyst
▴ 60
What do you suggest should i use ploidy 12 for each chromosomes for variant calling? Or using coverage information provided below can I det…
Comment: variant calling chromosome-wise from WGS data
by
analyst
▴ 60
**Chromosome Avg_Coverage** Chr10A.bam 55.49 Chr10B.bam 47.28 Chr10C.bam 46.83 Chr10D.bam 52.52 Chr10E.bam 38.16 …
Comment: error in reading codelink data
by
nazaninhoseinkhan
▴ 530
Thanks. I can be reached at hosseinkhan@ut.ac.ir.
Answer: Alternatives to WGCNA
by
LChart
4.9k
GLASSO, ARACNe-AP, and Megena are alternative co-expression frameworks that have been applied. However standard clustering methods should g…
Comment: How to visualize Combat-seq corrected counts
by
cfos4698
★ 1.1k
Are you sure you didn't use `ComBat` instead of `Combat_seq`?
Answer: RNA-seq analysis
by
Gordon Smyth
★ 8.0k
featureCounts is so fast that you simply try both strands on one of the BAM files. From R, just try: ``` library(Rsubread) fc1 <- featureCo…
Answer: Liquid Biopsy datasets
by
ehaag
▴ 20
You could try the NIAID Data Ecosystem: https://data.niaid.nih.gov/ It's designed to help researchers find datasets from infectious and …
Answer: RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitne
by
ehaag
▴ 20
Check out the NIAID Data Ecosystem, which aggregates datasets related to RNA viruses including HIV, Influenza, and SARS-CoV-2: https://data…
Answer: Metagenomics mock datasets
by
ehaag
▴ 20
If you're still looking, the NIAID Data Ecosystem is a discovery portal for reusable datasets: https://data.niaid.nih.gov/ It integrates d…
Answer: RNA-seq analysis
by
GenoMax
151k
> require strand specific information See the answers in --> https://www.biostars.org/p/9547560/ for tools that you can use with your alig…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
``` pheatmap(cent_expr_matrix, breaks = cent_expr_breaks, cluster_rows=F, cluster_cols=T, cellwidth = 10,cellheight=8.6, …
Answer: Using structure prediction approaches to predict interaction between two protein
by
Mensur Dlakic
★ 29k
> I am specifically looking for tools excelling without MSAs. I don't think there is such a tool that will excel at predicting protein i…
Answer: How to visualize Combat-seq corrected counts
by
ATpoint
88k
ComBat-seq does not produce negative counts but preserves the integer nature. Thats the whole point of the method. Lets see your code and d…
Comment: Heatmap of a transformed deseq object with pheatmap
by
SamGG
▴ 130
Glad it helps you. You probably can remove the legend and color scale, or if you save the figure in PDF or SVG (I don't know whether SVG is…
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