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85 results • Page
2 of 2
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0
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442
views
Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies
microbialassociationnetworks
metatranscriptomics
metagenomics
netowrkbiology
4 days ago by
sebasar1245
• 0
0
votes
1
reply
110
views
Bed file
bedfile
updated 4 days ago by
Pierre Lindenbaum
160k • written 4 days ago by
Jeet
• 0
0
votes
0
replies
74
views
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
R
AUC
genes
hub
validation
4 days ago by
wyt1995
▴ 30
0
votes
0
replies
83
views
Toxinpred 3.0 tool
peptide
protein
toxin
toxicity
updated 4 days ago by
zx8754
11k • written 4 days ago by
Saurabh
• 0
0
votes
3
replies
216
views
Microarray pbrobe ID to gene ID problem
microarray
updated 3 days ago by
GenoMax
140k • written 4 days ago by
mnx0723
• 0
0
votes
0
replies
91
views
Polysome profiling data
Polysome
updated 4 days ago by
Ram
43k • written 5 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
99
views
What to do with multiple genes in ballgown?
STAR
ballgown
DESeq2
5 days ago by
markusz
▴ 10
1
vote
9
replies
412
views
miRNA alignment with Bowtie2
bowtie2
3 days ago by
Chironex
▴ 40
0
votes
0
replies
83
views
Difference between reading concatenated PE reads into jellyfish and merging paired end .jf outputs independently
Jellyfish
Kmer
GenomeScope
5 days ago by
joshua.j.wright
▴ 10
0
votes
1
reply
132
views
Longitudinal microbiome study - Pooling of data?
longitudinal-microbiome-study
statistics
updated 5 days ago by
Chris Dean
▴ 390 • written 5 days ago by
laura_g
• 0
0
votes
0
replies
95
views
ImmuCellAI
RStudio
ImmuCellAI
updated 5 days ago by
Ram
43k • written 5 days ago by
sana
• 0
0
votes
2
replies
179
views
Is there a program that can predict the sequence of an organisms telomeres just from raw sequencing reads
telomeres
genomics
sequencing
5 days ago by
Mark
• 0
0
votes
1
reply
123
views
Calculating (Groupwise) Log2fold change using values obtained from SST-RMA?
SST-RMA
genes
TAC
thermofisher
foldchange
updated 5 days ago by
ATpoint
81k • written 5 days ago by
purple909
• 0
0
votes
0
replies
96
views
Issue to run gatk4 spark
gatk
spark
5 days ago by
Mojtaba
• 0
2
votes
5
replies
580
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 4 days ago by
jkbonfield
★ 1.2k • written 5 days ago by
K
• 0
0
votes
1
reply
137
views
SNP and Genes position matching dataframes in R
R
dataframe
updated 5 days ago by
dthorbur
★ 1.6k • written 5 days ago by
QX
• 0
0
votes
1
reply
150
views
Alignment tool of repeat expansion detection
STR
NGS
readexpansion
updated 5 days ago by
Jesse
▴ 740 • written 5 days ago by
adarsh_pp
▴ 40
2
votes
7
replies
498
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 5 days ago by
Chris Dean
▴ 390 • written 6 days ago by
ev97
▴ 20
0
votes
0
replies
119
views
HADDOCK 2.4
Protein
Docking
6 days ago by
Preeti
• 0
1
vote
5
replies
231
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 6 days ago by
Haci
▴ 520 • written 6 days ago by
kayah
• 0
1
vote
3
replies
251
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 6 days ago by
GenoMax
140k • written 6 days ago by
Matt
• 0
0
votes
0
replies
103
views
SAMstat mapping quality report MAPQ gt vs MAPQ lt
Sequencing
mapping
samstat
6 days ago by
njornet
▴ 10
3
votes
3
replies
378
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 6 days ago by
Ram
43k • written 7 days ago by
Samuel
▴ 20
1
vote
4
replies
244
views
Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
6 days ago by
feather-W
• 0
2
votes
4
replies
236
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 6 days ago by
Michael
54k • written 6 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
104
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
6 days ago by
CTLong
▴ 90
0
votes
0
replies
93
views
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
SPAdes
unmapped_reads.
assembly.
MaSuRCA.
6 days ago by
Sony
▴ 10
0
votes
5
replies
340
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
6 days ago by
Maxwell
• 0
1
vote
9
replies
762
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 6 days ago by
Dave Carlson
★ 1.6k • written 7 days ago by
Matthew
• 0
2
votes
7
replies
478
views
Need a link to OLDERADO server
pdb
protein
nmr
structure
6 days ago by
b2003
• 0
0
votes
4
replies
329
views
Can I perform a Functional Enrichment Analysis on a specific list of pre-defined genes?
RNA-seq
DGE
1 day ago by
Adam
• 0
0
votes
11
replies
618
views
Filtering VCF based on codon-transcript
vcf
bcftools
updated 2 days ago by
barslmn
★ 2.1k • written 13 days ago by
avelarbio46
▴ 30
0
votes
7
replies
422
views
Using VEP annotation output as the input for a second VEP annotation
VCF
VEP
Annotation
updated 6 days ago by
Ram
43k • written 6 weeks ago by
Arton
• 0
0
votes
10
replies
734
views
Problem running scPred
scPred
scPredict
updated 5 days ago by
Ram
43k • written 10 weeks ago by
Nitin
• 0
0
votes
8
replies
1.4k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 4 days ago by
xiangbinruan
• 0 • written 18 months ago by
Phoebe Magdy
• 0
85 results • Page
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Recent Votes
Answer: Before or after LD clumping for PRS calculation in GWAS
Comment: CAZy database has multiple family sequence...
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
Answer: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
Comment: Differential express genes in imbalance groups
Answer: Differential express genes in imbalance groups
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Recent Replies
Comment: Before or after LD clumping for PRS calculation in GWAS
by
경준
▴ 20
1. I think i misunderstood logistic regression of association test. 2. you're right. Thank you for your helpful reply sam!
Comment: library(scater)
by
Mensur Dlakic
★ 26k
> I am not able to install the package scater as per the webpage I urge you to read back what you wrote and think whether you'd be able to…
Comment: How to corrected test statistics based on the LDSC intercept?
by
Isaac
• 0
Thank you very much!
Comment: Transcription Start Site
by
Ming Tommy Tang
★ 3.8k
you can use bioconductor as shown in this post using Genomicanges https://support.bioconductor.org/p/46508/
Comment: scRNAseq normalization
by
Ming Tommy Tang
★ 3.8k
To be honest, I really do not use SCT, and use log normalization all the time...
Comment: Subsetting Seurat object based on list of cell barcodes
by
Ming Tommy Tang
★ 3.8k
index<- rownames(seurat.obj_combined) %in% all_good_cells_rhemac10$V1 seurat.obj_combined[index, ] should do the trick
Comment: Average expression of a sample in single-cell data
by
dsull
★ 5.6k
Well, if you're only sequencing the very end (the 3' end) of transcripts, how are you going to detect any of the splice junctions that appe…
Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
by
swbarnes2
14k
> Seems like pooling all should be statistically more robust. Yup. So put everything into the same DESeq2 object. See: https://…
Answer: Expert Guidance Required for De Novo Transcriptome Analysis
by
Doomhammer
• 0
Do you have enough clean data to assemble, for each genotypes independently? I think at first we should find the difference in transcripts …
Answer: Downloading epigenetic and mutation data of specific TCGA BRCA samples
by
aUser
▴ 30
Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:…
Comment: error in wigToBigWig while converting mappability to bedgraph
by
Dora
▴ 10
Thank you so much for your reply! here is what I have after entering the command variableStep#chrom=NT_173277.1 Cavia porcellus strain…
Comment: Differential express genes in imbalance groups
by
Chris
▴ 260
Wow, the author of the tool reply. Thank you so much!
Comment: t-test in two groups, multiple rows
by
sooni
▴ 20
It was my mistake. I converted the dataframe to matrix. It works! Thank you!
Comment: Differential express genes in imbalance groups
by
Gordon Smyth
★ 6.9k
I do mean the quality of each sample (as measured by residual variability in the linear model, in other words by consistency with other sam…
Comment: Differential express genes in imbalance groups
by
Chris Dean
▴ 390
That sounds super interesting. I have never heard of this approach before. When you say 'sample quality weights' are you referring to dif…
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