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396 results • Page 4 of 8
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votes
2
replies
176
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Longitudinal analysis of subpopulations: which approach is better?
differential-expression DEG model
14 days ago by Lluís R. ★ 1.2k
0
votes
2
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260
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Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
6 days ago by sainavyav22 • 0
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma Batch-effect MDS Galaxy
updated 27 days ago by 43k • written 4.8 years ago by • 0
2
votes
2
replies
304
views
How to row normalize a matrixplot?
scRNA-seq RNA-seq single-cell scanpy
28 days ago by bioinfo ▴ 150
0
votes
2
replies
314
views
bam merging for archaic samples
samtools bam
updated 22 days ago by 43k • written 23 days ago by ▴ 100
0
votes
1
reply
599
views
Basic stats in hierfstat
Fst stats hierfstat
updated 12 days ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
111
views
consensus sequence calling
consensus
updated 15 hours ago by ★ 2.4k • written 19 hours ago by • 0
0
votes
1
reply
198
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 12 days ago by 19k • written 13 days ago by • 0
0
votes
1
reply
187
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 20 days ago by ★ 27k • written 20 days ago by • 0
1
vote
1
reply
104
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 18 hours ago by 8.6k • written 19 hours ago by ▴ 30
0
votes
1
reply
181
views
unable to get feature count results
featureCounts
updated 13 days ago by 43k • written 13 days ago by • 0
1
vote
1
reply
208
views
Failed kmer content
kmer illumina ngs
updated 20 days ago by 43k • written 21 days ago by • 0
0
votes
1
reply
223
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 28 days ago by ★ 2.4k • written 28 days ago by • 0
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 25 days ago by 43k • written 6.7 years ago by ▴ 80
0
votes
1
reply
207
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 20 days ago by ★ 2.4k • written 20 days ago by • 0
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 26 days ago by 43k • written 6.2 years ago by ▴ 40
0
votes
1
reply
305
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 26 days ago by 142k • written 26 days ago by • 0
0
votes
1
reply
245
views
merging Seurat objects after SCT
Seurat SCT
updated 28 days ago by 43k • written 28 days ago by • 0
0
votes
1
reply
173
views
Identification of Transgene insertion sites
Transgene Whole-Genome-Sequencing transgene-sites
updated 21 days ago by 43k • written 21 days ago by • 0
0
votes
1
reply
529
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 18 days ago by • 0 • written 5 months ago by • 0
0
votes
1
reply
177
views
Alignment of samples with spike-in
alignment multimapping RNA-seq ChIP-seq spike-in
updated 3 days ago by 142k • written 3 days ago by • 0
0
votes
1
reply
243
views
Subsetting and merging back Seurat Object brings different results
Seurat
11 days ago by Bine ▴ 60
0
votes
1
reply
220
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK recalibration
updated 12 days ago by 142k • written 12 days ago by ▴ 30
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect R
updated 26 days ago by 43k • written 6.1 years ago by • 0
0
votes
1
reply
191
views
Differential Accessibility
DiffBind
updated 14 days ago by 43k • written 14 days ago by • 0
0
votes
1
reply
229
views
Finding batch and outlayers
Pca
updated 14 days ago by ▴ 460 • written 15 days ago by • 0
0
votes
1
reply
157
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq nucleosome fragment
updated 21 days ago by 82k • written 21 days ago by • 0
0
votes
1
reply
317
views
Could you please assist in identifying this cluster?
single-cell
updated 24 days ago by 43k • written 24 days ago by ▴ 40
0
votes
1
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696
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 13 days ago by 43k • written 13 days ago by • 0
1
vote
1
reply
441
views
ComBat_Seq stuck adjusting the data
Batch-Effect RNAseq ComBat-Seq
updated 4 days ago by • 0 • written 4 months ago by ▴ 10
0
votes
1
reply
144
views
input file for alternative splicing in rmats in linux
rmats
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
1
reply
205
views
Subset Seurat object from Xenium spatial data
Seurat Xenium Spatial
updated 20 days ago by ★ 2.4k • written 20 days ago by ▴ 110
0
votes
1
reply
227
views
Annotating a dataset with gnomAD v4 using Hail
Python Sequencing Hail Exome Annotation
updated 26 days ago by ▴ 40 • written 26 days ago by • 0
1
vote
1
reply
152
views
Discrepancy in read counts from fastq
downsampling fastq
updated 11 days ago by 43k • written 11 days ago by ▴ 100
1
vote
1
reply
452
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 23 days ago by ★ 7.1k • written 25 days ago by ▴ 280
0
votes
1
reply
280
views
Two databases: Human Microbiome Project and MGnify
Microbiome databases
updated 28 days ago by 142k • written 28 days ago by ▴ 360
0
votes
1
reply
193
views
RNA-seq bacteria contamination
RNA-seq
updated 21 days ago by 142k • written 21 days ago by • 0
0
votes
1
reply
555
views
HOMER on AWS
HOMER
updated 11 days ago by • 0 • written 2.2 years ago by ★ 1.4k
1
vote
1
reply
260
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 18 days ago by 82k • written 18 days ago by • 0
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome PCA batch-effect SNP
updated 26 days ago by 43k • written 4.8 years ago by ▴ 90
0
votes
1
reply
18
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp filteration genotype quality GATK
updated 20 minutes ago by 161k • written 1 hour ago by • 0
0
votes
1
reply
167
views
tbtool
tbtool
updated 21 days ago by 43k • written 21 days ago by • 0
1
vote
1
reply
255
views
Retrieve a % coverage for each transcript
RNA-seq
updated 26 days ago by 43k • written 26 days ago by ▴ 40
0
votes
1
reply
233
views
Help with DGEList function
DGEList R
updated 8 days ago by ▴ 100 • written 9 days ago by • 0
1
vote
1
reply
667
views
Save experiment with batch effects - Protein microarray
statistics protein-array batch-effect
updated 27 days ago by 43k • written 4.4 years ago by ▴ 10
1
vote
1
reply
208
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
29 days ago by CTLong ▴ 110
0
votes
1
reply
250
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort. SAMtools. BAM. SAM.
updated 6 days ago by 142k • written 6 days ago by ▴ 10
1
vote
1
reply
204
views
Help/Direction Needed for Data Analysis of RNA
Sequencing RNA-seq DNA-Seq
updated 27 days ago by ★ 6.0k • written 27 days ago by • 0
1
vote
1
reply
167
views
student
epitranscriptomics
updated 6 days ago by 82k • written 6 days ago by • 0
0
votes
1
reply
1.2k
views
Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
random-effects RNA-Seq batch-effect
updated 27 days ago by 43k • written 6.8 years ago by • 0
396 results • Page 4 of 8
Recent Votes
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
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Recent Replies
Comment: BWA alignment by ATpoint 82k
That is not what the logs above tell, but good you solved it.
Answer: Inquiry about deseq2 transformation by ATpoint 82k
The transformations first correct for sequencing depth (and [composition][1]) and then apply the variance stabilization / regularization. N…
Answer: The total expressed genes in RNA-Seq data by ATpoint 82k
There is no robust definition of "expressed" genes, this has been asked many times before. edgeR doesn't care about "expressed", it cares (…
Answer: What is the bin size for Bamcompare? by ATpoint 82k
It is the number of adjacent bases that are aggregated (binned) into a single value. I find binning not optimal, and would always set this …
Comment: Is it necessary to do genotype quality filteration after snp calling with GATK by Pierre Lindenbaum 161k
see VQSR https://gatk.broadinstitute.org/hc/en-us/articles/360035531612-Variant-Quality-Score-Recalibration-VQSR and https://gatk.broadinst…
Comment: Snakemake wrapper issue by Matvii Mykhailichenko • 0
Hi, I kind of did and kind of didn't: I stopped trying to use snakemake( I remember that it's a lot of hustle to install pickard, maybe you…
Answer: Is there any way to modify this pie chart ? by marco.barr ▴ 100
Hi, you can add the labels outside chart using `geom_label_repel` from `ggrepel` package. Check out this guide [https://r-charts.com/part…
Answer: Snakemake wrapper issue by Wei-Chen Pan • 0
Hi, did you solve your problem ? I also encounter same issue but it's `wrapper:"v3.9.0/bio/picard/mergevcfs"`. In my log file, it said:…
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results? by 林明德 • 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11 by Ashfaq • 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results? by GenoMax 142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation by GeneC • 0
Thank you for the link and details
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