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120,972 results • Page
6 of 2420
Sort: Rank
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Replies
3
votes
0
replies
233
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Herald:
The Biostar Herald for Wednesday, March 19, 2025
herald
25 days ago by
Biostar
3.4k
0
votes
0
replies
176
views
Cosmic database update issue in annovar
annovar
cosmic
genomics
updated 25 days ago by
Ram
45k • written 25 days ago by
abhijitswain
• 0
1
vote
1
reply
351
views
Transforming diploid GT on male X and Y chromosome to haploid
VCF
genotype
gVCF
25 days ago by
Michaela
▴ 10
3
votes
2
replies
336
views
How do I figure out pangenome location of hg38 coordinates?
pangenome
hg38
vg
25 days ago by
a5864557
▴ 10
5
votes
7
replies
573
views
How I can curate all exon start-end positions for 50 genes (to create GTF file)?
gtf
curation
gene
updated 24 days ago by
GenoMax
150k • written 26 days ago by
Esra
▴ 10
0
votes
0
replies
172
views
generating manhattan plot through hail
plot
manhattan
hail
visualizations
gwas
25 days ago by
nitya
• 0
0
votes
0
replies
164
views
Hard Filtering Differences between WES and WGS
WES
WGS
Hard-Filtering
updated 25 days ago by
Ram
45k • written 26 days ago by
SIMONE
• 0
0
votes
3
replies
344
views
Am I accounting for replicates correctly in pseudobulk analysis?
deseq2
single-cell
pseudobulk
updated 25 days ago by
ATpoint
87k • written 26 days ago by
Aspire
▴ 370
2
votes
4
replies
473
views
Is there too little variation to detect meaningful gene changes?
DESEQ
updated 26 days ago by
Istvan Albert
102k • written 27 days ago by
Megan
▴ 50
3
votes
5
replies
450
views
nanopore SNV callers returns empty VCF
snv_caller
nanopore
updated 19 days ago by
Istvan Albert
102k • written 26 days ago by
Meghan.T
▴ 10
15
votes
3
replies
1.2k
views
Tutorial:
Avoiding the Pitfalls of the Anaconda License: A Practical Guide
conda
Anaconda
license
25 days ago by
Juke34
9.2k
0
votes
2
replies
280
views
How many cells are needed in subcluster to draw conclusions?
immunology
T-cells
scRNA-seq
24 days ago by
S
• 0
0
votes
2
replies
267
views
Question about assigning gene names, tximport and DESeq2
tximport
deseq2
2 days ago by
bioinfo
▴ 150
3
votes
3
replies
380
views
RNASeq: Confused about adapters with barcodes and seq company's filtering
atria
rnaseq
adapter-trimming
updated 24 days ago by
GenoMax
150k • written 26 days ago by
Davor
• 0
1
vote
2
replies
309
views
VEP won't show symbols for all variants; SnpEff will, but won't for others
vep
snpeff
updated 26 days ago by
Jeremy Leipzig
23k • written 27 days ago by
mary.v.volkova
▴ 20
0
votes
2
replies
254
views
How to plot LMER estimate values in heatmap ?
cell
scRNAseq
TF
lmer
transcription
25 days ago by
carolofharvest
▴ 50
1
vote
2
replies
1.3k
views
News:
Final Call - Next-Generation Sequencing Data Analysis: A Practical Introduction (April 2-4 in Munich) - Only 2 seats left
Workshop
RNAseq
Variant-Calling
Illumina
DNAseq
26 days ago by
ecSeq Bioinformatics
▴ 10
0
votes
1
reply
224
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
tehnical-replicates
DESeq2
RNA-Seq
updated 26 days ago by
Ram
45k • written 26 days ago by
hellothere
• 0
0
votes
3
replies
341
views
Can anyone help me download the dbSNP data for Bos taurus ARS-UCD1.3?
GWAS
genetics
WGS
updated 23 days ago by
Ram
45k • written 26 days ago by
K
• 0
0
votes
1
reply
240
views
Co-expression analysis of miRNAs and target mRNAs
miRNA
targets
co-expression
miRNA-mRNA
updated 26 days ago by
i.sudbery
21k • written 27 days ago by
baibhu1234
▴ 40
0
votes
0
replies
169
views
Beagle Imputation
Beagle
Imputation
27 days ago by
mahlet.teka
• 0
0
votes
0
replies
278
views
Issue with bam-readcount and fpfilter.pl: Saying "failed to get readcounts for variant allele"
bam-readount
somaticsniper
updated 27 days ago by
Pierre Lindenbaum
166k • written 27 days ago by
1phamcha2
• 0
2
votes
2
replies
299
views
miRNA-seq: QC reports and workflow
miRNA-seq
ION-Torrent
RNA-seq
FASTQC
26 days ago by
omicon
▴ 40
1
vote
0
replies
155
views
How to Run Large-Scale Foldseek Comparisons (Human vs. C. elegans)
c.elegans
Foldseek
Genes
Orthologs
Homologs
27 days ago by
bioinformatics_rk
▴ 10
0
votes
1
reply
263
views
Recommendations for Reference-guided de novo assembly assembly approaches or pipelines?
ont
assembly
wgs
nanopore
genomics
updated 27 days ago by
shelkmike
★ 1.5k • written 28 days ago by
Mark
▴ 30
0
votes
1
reply
236
views
Per Base Sequence Content FastQC
RNA-seq
quality-control
updated 27 days ago by
shelkmike
★ 1.5k • written 27 days ago by
Ariadna
▴ 20
3
votes
2
replies
360
views
Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transcriptomics
Data-Integration
Differential-Analysis
Transcriptomics
Data-Normalization
26 days ago by
Riley J
• 0
2
votes
3
replies
327
views
Population genetics with mutect2 data
haplotypecaller
mutect2
updated 25 days ago by
LauferVA
4.7k • written 27 days ago by
slzr_
• 0
1
vote
2
replies
265
views
ggplot of two data set with different colors
geom_line
scale_colour_manual
ggplot2
updated 27 days ago by
Watermelon
• 0 • written 27 days ago by
gogeni5529
▴ 60
1
vote
2
replies
273
views
Gene to use for phylogenic analysis
phylogenic-analysis
updated 27 days ago by
Ram
45k • written 27 days ago by
uttkarsh
• 0
0
votes
0
replies
153
views
Chrom3D
chrom3d
interchromosomal
genome
model
27 days ago by
desptsp
• 0
0
votes
1
reply
201
views
Scanpy use with reticulate in R : var_group_positions argument set up
R
Reticulate
Scanpy
27 days ago by
ZheFrench
▴ 590
1
vote
3
replies
290
views
CPTAC Data analysis
CPTAC
proteomics
updated 27 days ago by
LauferVA
4.7k • written 27 days ago by
jain72744
▴ 10
78
votes
13
replies
41k
views
10 follow
hg19 Centromere Position and Chromosome Length
centromere
ucsc
updated 27 days ago by
Ram
45k • written 14.6 years ago by
Jdk
▴ 260
0
votes
3
replies
298
views
How to Process Multiple SRRs for the Same BioSample ?
GEO
RNA-seq
NCBI
miRNAs
RNA
updated 27 days ago by
GenoMax
150k • written 27 days ago by
omicon
▴ 40
0
votes
3
replies
294
views
Methylation cpg probes annotation
annotation
methylation
cpg
TCGA
updated 27 days ago by
GenoMax
150k • written 27 days ago by
jain72744
▴ 10
1
vote
2
replies
363
views
How to convert .ab1 to fastq
Fastq
updated 27 days ago by
size_t
▴ 120 • written 29 days ago by
dr.suvarnakapale
• 0
0
votes
1
reply
220
views
How to deal with missing annotations in RNASeq data?
eggnogmapper
RNASeq
updated 27 days ago by
dthorbur
★ 2.9k • written 27 days ago by
v.berriosfarias
▴ 140
0
votes
2
replies
263
views
Why protein sequence from AUGUSTUS can't find in blast
genome
AUGUSTUS
galaxy
annotation
26 days ago by
Jl
• 0
1
vote
2
replies
255
views
How to make amazing UMAP to spatialPlot GIF
umap
spatial
27 days ago by
noodlejackson
▴ 40
1
vote
1
reply
204
views
Software for visualizing mass spectromety spectra
MS
Mass
Spectrometry
updated 25 days ago by
Joe
22k • written 28 days ago by
emalekos
▴ 40
1
vote
2
replies
291
views
Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation Detection
feedback
tool
27 days ago by
genanalyzer24
• 0
1
vote
1
reply
229
views
Detecting Aneuploidy from Bulk RNA-Seq Data
Aneuploidy
RNA-Seq
updated 27 days ago by
ATpoint
87k • written 28 days ago by
bioinfo1990
▴ 10
0
votes
0
replies
156
views
GSA genome studio call rate calculation issues
Genome
GSA
studio
29 days ago by
1769mkc
★ 1.2k
1
vote
2
replies
393
views
Parsing BAM file per cell from Smart-Seq2 dataset
starsolo
star
BAM
smartseq2
alignment
updated 29 days ago by
dsull
★ 7.3k • written 4 weeks ago by
brutonk
• 0
0
votes
0
replies
198
views
News:
Spring School in Bioinformatics - online, March 31 to April 4
Singularity
NGS
RNAseq
Phylogenomics
Docker
29 days ago by
Physalia-courses
★ 2.6k
2
votes
2
replies
387
views
Gene Expression Timeline Analysis for N=1
Analysis
Gene
Expression
27 days ago by
ATRX
★ 1.2k
0
votes
1
reply
539
views
Interactive UMAP for scRNA-seq Data
HTML
RMarkdown
Interactive-UMAP
scRNA-seq
updated 29 days ago by
S
• 0 • written 8 weeks ago by
s
• 0
0
votes
0
replies
200
views
Converting PLINK GWAS Summary Statistics (--glm) to BED Format for UCSC Liftover
PLINK
LiftOver
PLINK2
BED
GWAS
28 days ago by
Mllepnos
• 0
3
votes
0
replies
213
views
Tool:
PAN-GO Functionome: known functions of all human protein-coding genes
goenrichment
function
GO
goterms
geneontology
4 weeks ago by
geneontologyhelp
▴ 470
120,972 results • Page
6 of 2420
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Comment: ONT Live-Basecalling Issue?
by
GenoMax
150k
Did this block eliminate itself over time? It looks like ~4 M initial reads in your run are in "paused" state. Have not heard of this happe…
Answer: Is a log2 transformation an essential step in preparing expression data for mach
by
Mensur Dlakic
★ 29k
> Is a log2 transformation an essential step in preparing the expression data for machine learning, or can the normalized raw expression da…
Comment: How to re-annotate the structure of gene against a known genomic file
by
Mensur Dlakic
★ 29k
If you look above from this writing, this question was asked 5.9 years ago. If you click on user's name, you will see that they last visite…
Comment: Is a log2 transformation an essential step in preparing expression data for mach
by
Sib
▴ 60
I would greatly appreciate it if you could refer me to a tutorial on conducting feature selection for microarray data using some (or all) o…
Comment: Identify gene from sequence at scale in non-model organisms
by
shelkmike
★ 1.5k
I don't understand why you think that you need some gene names to perform GO annotation. Just upload your proteins to PANNZER. It is an onl…
Comment: How to re-annotate the structure of gene against a known genomic file
by
Olayemi F.
• 0
Hey Kanoo, How did this later turn out for you?
Comment: Batch effect
by
Fatemeh
▴ 40
Thanks very much.
Comment: Is a log2 transformation an essential step in preparing expression data for mach
by
ATpoint
87k
You're shooting buzz words as in the question before. Please read the underlying literature and follow guided tutorials. There is no genera…
Comment: TPM vs FPKM divergence at high values
by
ATpoint
87k
Please show the functions to calculate this. Both transformations are simple division and multiplication operations with the column sums of…
Comment: Is Centering and Scaling Essential for Expression Data as Input for Machine Lear
by
Sib
▴ 60
Sorry, is log2 taransformation also needed? Or we can apply ML methods on expression data without it?
Comment: TPM vs FPKM divergence at high values
by
pinheirofabiano
▴ 110
I don't have a better mathematical explanation, but FPKMs are not reliable for gene expression studies, there are many discussions about t…
Comment: TPM vs FPKM divergence at high values
by
megancgrdnr
• 0
Thank you for your answer! Do you have any sense of why the expression values diverge at higher-expressed genes? I can't see anything in th…
Comment: What does vg autoindex mpmap do?
by
Jordan M Eizenga
▴ 690
GCSA indexing certainly can be time consuming. On a reasonably well-behaved graph (such as those derived from VCFs, or usually those from t…
Comment: WGCNA
by
1769mkc
★ 1.2k
what your gene expression matrix size or dimension?
Answer: WGCNA
by
PFSXR
• 0
There are too few valid genes in the input matrix expr_filtered, possibly because after the goodSamplesGenes filtering, only the grey modul…
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