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1,000 results • Page 2 of 20
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1
vote
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161
views
Harmony integration PC variance explained
scRNA integration harmony
updated 1 day ago by ▴ 20 • written 4 days ago by • 0
0
votes
3
replies
229
views
merged rs number information
merged dbsnp
3 days ago by sskimvd • 0
1
vote
1
reply
163
views
Beginner differential methylation analysis
Methylation
updated 3 days ago by ★ 1.9k • written 4 days ago by ▴ 30
2
votes
1
reply
236
views
EnhancedVolcano underrepresenting DEGs
R
updated 2 days ago by 86k • written 4 days ago by ▴ 30
0
votes
0
replies
111
views
[maftools]Too many multi_hit and missense mutation
maftools gatk MAF data WES VCF
4 days ago by jiazheng_lin • 0
0
votes
0
replies
124
views
Negative F statistics for sex check in plink
plink check sex
4 days ago by kl ▴ 10
0
votes
1
reply
193
views
Chipseq peak calling and peak frequency region
chipseeker macs2
updated 3 days ago by 3.2k • written 5 days ago by ▴ 10
0
votes
1
reply
247
views
issue in RNA -seq analysis
NGS RNA-Seq
updated 5 days ago by 136k • written 5 days ago by • 0
0
votes
3
replies
341
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA deconvolution Music Music2 bulk
updated 5 days ago by 78k • written 6 days ago by • 0
0
votes
0
replies
226
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
6 days ago by Wenke • 0
0
votes
3
replies
301
views
Annovar - Annotated file cells show string
annovar
6 days ago by Roshan • 0
0
votes
1
reply
242
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW MinION Nanopore
updated 6 days ago by 136k • written 6 days ago by ▴ 40
0
votes
1
reply
214
views
htShinyExample-5.3 - not working
htShiny Oncoprint InteractiveComplexHeatmap
updated 1 day ago by 41k • written 6 days ago by ▴ 60
0
votes
0
replies
157
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA Worms RNA-Seq
6 days ago by kdca • 0
0
votes
3
replies
273
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
6 days ago by Sara ▴ 230
0
votes
0
replies
879
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics telomeres reads
6 days ago by Mark • 0
0
votes
0
replies
155
views
not best k value found
de assemblly assembly novo kmergenie
6 days ago by shaileshdesai76 • 0
0
votes
0
replies
166
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR ribo-seq multi-mapped rna-seq TE
7 days ago by Carmen • 0
0
votes
0
replies
170
views
Identifying differentially expressed loci for gene duplicates using DESeq2
rna-seq deseq2
7 days ago by pl23 • 0
0
votes
2
replies
285
views
Find Genes in Homer Analysis that have the enriched Motif
single ORA nucleus mRNA Homer
2 days ago by je71xusa • 0
0
votes
2
replies
275
views
Tool to get genes in the neighbourhood of a particular gene
locus Gene
updated 7 days ago by ★ 1.3k • written 7 days ago by ▴ 80
2
votes
9
replies
655
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR Salmon mapper aligner RNAseq
1 day ago by ian.will ▴ 10
5
votes
2
replies
245
views
RNA Contamination Tool for Developing Cell Samples
contamination scRNA quality RNA SoupX
6 days ago by Rafael Soler ★ 1.2k
1
vote
2
replies
199
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole genome assembly sequencing
updated 7 days ago by 47k • written 7 days ago by ▴ 10
1
vote
0
replies
140
views
What are the methods to correlate/study metabolomics data to proteomics data?
metabolomics proteomics multiomics
8 days ago by WUSCHEL ▴ 720
0
votes
3
replies
296
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R complexheatmap
updated 2 days ago by ★ 1.2k • written 8 days ago by ▴ 10
0
votes
0
replies
112
views
Find equivalent pathways between KEGG, Reactome, and WikiPathways
pathway mapping database
8 days ago by Ngrin • 0
0
votes
0
replies
126
views
GenAlEx Haploid Data Detecting Recombination
GenAlEx Popgen Haploid Recombination
8 days ago by turcoa1 • 0
0
votes
0
replies
130
views
TF Footprinting using HINT ATAC module from RGT
hintatac footprinting rgttoolbox atacseq
8 days ago by alphaflylizard • 0
0
votes
2
replies
261
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation Variant proteomics FASTA VCF
7 days ago by chscho • 0
0
votes
0
replies
118
views
Trouble making a ggmsa alignment plot
R ggmsa
8 days ago by andre.arrudalima ▴ 30
0
votes
0
replies
112
views
cNMF vs LIGER
NMF correction batch
8 days ago by e.r.zakiev ▴ 170
1
vote
4
replies
301
views
Analyze with Geo2R
R NCBI
6 days ago by anasjamshed ▴ 120
0
votes
0
replies
869
views
For people doing high molecular weight DNA sequencing library prep, do you see a steep drop off in the fragment sizes before and after the library pr…
library-prep sequencing ont nanopore ngs
8 days ago by Mark • 0
0
votes
0
replies
129
views
Creating heatmap for ChIP-seq using deeptools
heatmap chipseq chip deeptools visualization
8 days ago by biology_inform ▴ 50
0
votes
1
reply
138
views
error in plink
polygenicriskscore prscalculation prs plink error
updated 8 days ago by ★ 1.1k • written 8 days ago by • 0
0
votes
2
replies
209
views
how to use pilon
genome pipelines assembly pilon contig
updated 3 days ago by 3.2k • written 8 days ago by • 0
3
votes
2
replies
241
views
t-test by row
R t-test
updated 8 days ago by ▴ 880 • written 9 days ago by ▴ 10
0
votes
0
replies
110
views
jellyfish histo is empty
jellyfish kmer fastq
9 days ago by m.t.lorenc • 0
0
votes
0
replies
123
views
Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
giraffe surject vg
9 days ago by cassiwatt • 0
1
vote
2
replies
209
views
How to identify the nearest gene associated with a specific SNPs?
RSID GWAS
updated 9 days ago by ▴ 840 • written 9 days ago by ▴ 150
0
votes
1
reply
168
views
WGCNA convenience function
WGCNA
updated 8 days ago by 3.5k • written 9 days ago by • 0
0
votes
0
replies
120
views
Low mapping after Cufflinks assembly
assembly gffread cuffmerge Cufflinks RSEM
9 days ago by sofiablancoglez • 0
0
votes
0
replies
115
views
KEGG module and abundance of its KEGG Orthologs for functioning
function kegg abundance
9 days ago by Jonathan Yoou ▴ 60
1
vote
4
replies
278
views
Deseq2 5 level condition - building contrast
rna-seq deseq2
updated 9 days ago by 78k • written 9 days ago by ▴ 10
0
votes
0
replies
114
views
RNASeq vs TermSeq
RNAseq statistics TermSeq
9 days ago by npb27 • 0
0
votes
0
replies
107
views
Best Preprocessing Approach for Tissue Microarray Data: Separate or Post-Merger Normalization?
normalization array
9 days ago by rk.khayami94 ▴ 10
0
votes
0
replies
112
views
Interpretation of mean-variance trend in voom
EdgeR Voom
updated 9 days ago by 41k • written 9 days ago by • 0
0
votes
0
replies
168
views
How to perform analysis with given copy number variation datasets between disease and control cohorts
CNV analysis
9 days ago by Tsin-Lau • 0
0
votes
0
replies
114
views
Pathview Enzyme Code to Gene Symbol Conversion
Pathview KEGG
10 days ago by B.N. • 0
1,000 results • Page 2 of 20
Recent Votes
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
Seurat integration of two datasets - GSE126783
about batch correction in scRNA-seq
How to compare two Seurat object (sample) in order to find top markers?
How do I resolve an integration error in Seurat?
The difference between merge and integration with Seurat objects
Analyzing single cell RNA seq with multiple samples and conditions
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Recent Replies
Comment: How can I map coordinates between two strains of yeast? by Jimmy ▴ 10
Yes (S. cerevisiae)
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by GenoMax 136k
> less than 100 for some samples Hmm. That is surprising but then in light of that fact ~20% recovery of cells does not sound bad.
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by newbee ▴ 40
Thanks for raising these valid points. I do not have the answer right now. Lately, I heard from the PI that they started with a small numbe…
Comment: How to get multiple protein domain database domain name from id's by GenoMax 136k
A list of InterPro domains is available: https://ftp.ebi.ac.uk/pub/databases/interpro/current_release/entry.list
Answer: DIAMOND tutorial by GenoMax 136k
`DIAMOND` has a wiki page: https://github.com/bbuchfink/diamond/wiki Links for DIAMOND papers are here: https://github.com/bbuchfink/diamo…
Comment: How to do simple pathway analysis? by AK ★ 2.2k
Hi [he1k](https://www.biostars.org/u/139817/), Please use the following script which downloads and parses the keg data on the fly: [keg_hi…
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison by CTLong ▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel by MohammadAlkadi ▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data by Kevin Blighe 86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down by ATpoint 78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down by Katie • 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations by AMARU • 0
Hey, did you solve it? I am having a very similar issue. Thanks
Answer: Bulk and Single Cell RNA-seq online course by swbarnes2 13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
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