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400 results • Page 6 of 8
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177
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BIOM format can contain tabular data ?
BIOM phyloseq biomformat R
28 days ago by chemokine-1 ▴ 10
0
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0
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900
views
Advice on group specific condition effect and model matrix in deseq2
deseq2 batch-effect
updated 29 days ago by 43k • written 4.1 years ago by ▴ 330
0
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0
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215
views
miRDeep2: How to get the read counts
mirdeep2
26 days ago by Atul K. • 0
0
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0
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155
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 23 days ago by 8.7k • written 23 days ago by • 0
0
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0
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190
views
RNA-seq: full length gene
RNA-seq
updated 18 days ago by 43k • written 19 days ago by • 0
0
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0
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196
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
27 days ago by P. • 0
0
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0
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1.9k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq gene-expression-matrix correlation R
updated 28 days ago by 43k • written 6.3 years ago by ▴ 30
0
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0
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209
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
25 days ago by DanielEB_fisk ▴ 20
0
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0
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150
views
Krona Pie-chart taxanomy IDs were not found warning. Taxonomy Classification Metagenomics
Classification Metagenomics Krona Kraken2
5 days ago by Aytaç • 0
0
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0
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102
views
How to get somatic variation based on RNA-seq data?
RNA-seq variation somatic
22 days ago by feather-W • 0
0
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0
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137
views
Add geno header to VariantAnnotation objects
nichenet scRNA-seq
29 days ago by QX • 0
0
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0
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147
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
15 days ago by Bine ▴ 60
0
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0
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227
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
22 days ago by Javier • 0
0
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0
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1.5k
views
minifi for RRBS
rrbs batch-effect methylation
updated 28 days ago by 43k • written 7.2 years ago by ★ 2.9k
0
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0
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99
views
monocle 3-- Could not get node in small cluster
monocle3
7 days ago by synat.keam ▴ 100
0
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0
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98
views
dbNSFP sift scores integration
SIFT VEP dbNSFP
1 day ago by atariw ▴ 10
1
vote
0
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153
views
.lgen file has 3+ different alleles
PLINK lgen ped
updated 9 days ago by 11k • written 11 days ago by ▴ 10
0
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0
replies
138
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
21 days ago by Kash ▴ 110
0
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0
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213
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
27 days ago by synat.keam ▴ 100
0
votes
0
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372
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
27 days ago by Ronin • 0
0
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0
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159
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 4 days ago by 43k • written 4 days ago by • 0
0
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0
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133
views
Mitogenomes gap closure and making circular genome
gapclosure Mitogenomes validation circulargenome
9 days ago by KHURRAM SHAHZAD • 0
0
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0
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142
views
vcf procesing for ML antigen prediction
formats vcf fastaq HLA_imputation HLA_typing
11 days ago by Javier • 0
0
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0
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168
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames RNA-Seq WGCNA unique
28 days ago by shasabhi1 • 0
0
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0
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283
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 22 days ago by 43k • written 14 months ago by ▴ 20
0
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0
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154
views
Automated internal stop codon checker
ORF stopcodon internal virus
29 days ago by Balazs Horvath ▴ 10
0
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0
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105
views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
13 days ago by Vijith ▴ 30
0
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0
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135
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer mutect variant-calling GATK somatic-variants
updated 14 days ago by 43k • written 14 days ago by • 0
0
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0
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134
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic Variant predisposition
11 days ago by mikemakaveli1 • 0
0
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0
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119
views
The concept of co-occurrence network structure
co-occurence microbiome network
21 days ago by ohtang7 ▴ 40
0
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0
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121
views
LEfSe
LEfSe
15 days ago by benkosta • 0
0
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0
replies
124
views
How to implement an IGV to streamlit app?
python streamlit igv
9 days ago by avigail.shnaider • 0
0
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0
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183
views
Designing single-stable RNA molecules
structure RNA
19 days ago by Edna • 0
0
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0
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95
views
Imputation advice
imputation
23 days ago by kl ▴ 10
0
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0
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117
views
Annotate VCF via VEP for gnomAD annotation considering FILTER column
vep vcf gnomad
6 days ago by asalimih ▴ 60
0
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0
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1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 26 days ago by 43k • written 4.1 years ago by • 0
1
vote
0
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164
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology RNA-seq R
updated 29 days ago by 43k • written 29 days ago by ▴ 10
0
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0
replies
134
views
Modify plot R mtDNA indel
plot mtDNA R
11 days ago by marco.barr ▴ 110
0
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0
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82
views
Is there a real ground truth for CNV data?
CNV
20 hours ago by jennyp0706 • 0
0
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0
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115
views
File with NCBI summary or Uniprot description
annotation visualisation NCBI Uniprot RNA
updated 21 days ago by 43k • written 22 days ago by • 0
0
votes
0
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119
views
Cox Model with interaction item interpretation
Cox
8 days ago by Bine ▴ 60
2
votes
0
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229
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
29 days ago by Alexander ▴ 220
0
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0
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135
views
Using limma in methylation EM-seq?
EM-seq methylation
15 days ago by Lluís R. ★ 1.2k
0
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0
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224
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 25 days ago by 43k • written 25 days ago by • 0
0
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0
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46
views
NEURON, Brian2, NEST, or PyNN
NEST NEURON PyNN Brian2
8 hours ago by brunofelicianodeomena • 0
0
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0
replies
108
views
meffil.snp.concordance
meffil methylation snp_concordance
7 days ago by kyj222637 • 0
0
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0
replies
120
views
Error while loading model of Spatial data deconvolution using cell2location
Python cell2location
updated 8 days ago by 43k • written 8 days ago by ▴ 50
0
votes
0
replies
113
views
Analysis of the gene family of a genome.
Genome gene-family
updated 22 days ago by 43k • written 22 days ago by ▴ 90
0
votes
0
replies
190
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics phylogenetic
updated 18 days ago by 43k • written 19 days ago by • 0
0
votes
0
replies
232
views
create genewise sync file in popoolation
popoolation
updated 26 days ago by 142k • written 26 days ago by • 0
400 results • Page 6 of 8
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p by ATpoint 82k
This has formally been investiated by a reputable group here: https://academic.oup.com/nar/article/42/11/e95/1442937 IIRC they think tha…
Comment: RNA seq analysis by Jacek ▴ 10
Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap by dariober 14k
> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
Comment: Applying the metacell2 algorithm using python by JACKY ▴ 140
I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
Comment: Using Cutadapt to trim adapters from paired-end small RNA sequence data by melissa.joubert • 0
Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype by schmince • 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by Esraa • 0
Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
that's great, but i believe the issue is related to stdin rather than index
Comment: BWA alignment by a.alnawfal.1992 ▴ 260
it is not!!
Comment: How to calculate coverage of Nanopore long read data? by Arton • 0
Thank you! I eventually used the information generated by three tools (samtools coverage+ mosdepth + NanoPlot).
Comment: Alphaphold 3 pLDDT coloring scheme in chimerax? by mbrav005 • 0
Thank you Sir! you are right my model is not very good. Do You know how I can improve the scores. Also I am able to color the structure by …
Comment: Polish a large genome with Pilon by sansan_96 ▴ 90
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