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121,907 results • Page 41 of 2439
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347
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WGCNA sample-data preprocessing order
gene-expression wcgna microarray network data-preprocessing
8 months ago by Reuben • 0
6
votes
3
replies
2.1k
views
drug sensitivity prediction
deseq2 oncopredict R drug
updated 8 months ago by • 0 • written 2.9 years ago by ▴ 130
1
vote
1
reply
505
views
VCFfiltering
VCF BCFtools FreeBayes
updated 8 months ago by ★ 1.7k • written 8 months ago by • 0
0
votes
0
replies
345
views
Analysis and Verification of Mathematical Equations in the Theory of Consciousness
Consciousness brian Neuron neurobiology
updated 8 months ago by 153k • written 8 months ago by • 0
0
votes
0
replies
363
views
Genetic Trio Phasing with EAGLE2 using hg38
trios haplotype phasing genetics
8 months ago by heskett ▴ 110
5
votes
3
replies
886
views
b37 liftover
b37 liftover
8 months ago by spesks • 0
0
votes
0
replies
400
views
Plugging output files from phyluce phasing workflow into Structure
phyluce uce bam phasing structure
8 months ago by gabe.somarriba • 0
0
votes
0
replies
407
views
gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
header pacbio bam basecaller gcpp
8 months ago by therosng • 0
1
vote
1
reply
565
views
circos ignoring the ticks and plots
diagram circos
updated 8 months ago by 153k • written 8 months ago by ▴ 60
3
votes
4
replies
1.1k
views
Strange offsetting in deeptools?
deeptools
8 months ago by Elijah ▴ 10
0
votes
4
replies
884
views
Merging gvcf files between Dragen and other calling tools
gvcf merge bcftools
7 months ago by tacrolimus ▴ 150
7
votes
6
replies
1.4k
views
Download SRA raw data using efetch
sra-toolkit efetch biopython
8 months ago by biofysikos • 0
0
votes
7
replies
1.2k
views
Issue with CIBERSORTx Error 139
CIBERSORTX docker error193
updated 8 months ago by ★ 19k • written 8 months ago by • 0
0
votes
0
replies
462
views
Repeat Modeler Database Generation
masker modeler genome fungus repeat
8 months ago by SomeOne ▴ 240
0
votes
1
reply
540
views
How to scale data matrix in Seurat
Scale
updated 8 months ago by ▴ 180 • written 8 months ago by • 0
0
votes
1
reply
602
views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly genoem fungus HiC sequencing
updated 8 months ago by 153k • written 8 months ago by ▴ 240
0
votes
1
reply
435
views
Box plot of gene expression data
boxplot
updated 8 months ago by 89k • written 8 months ago by ▴ 10
1
vote
3
replies
1.1k
views
Questions regarding GSEA - clusterProfiler
RNA-seq GSEA
updated 7 months ago by ★ 2.0k • written 8 months ago by ▴ 10
0
votes
0
replies
434
views
Account for Clinical Variables in RNA-Seq Analysis
edgeR Batch effect
8 months ago by fabian ▴ 10
1
vote
4
replies
890
views
bioinformatics tutorial on Oxford Nanopore Technologies
oxford nanopore
updated 8 months ago by 153k • written 8 months ago by ★ 1.4k
6
votes
0
replies
1.1k
views
Tutorial: Step by step tutorial to replicate a genomics figure
R Unix ChIP-seq bioconductor
8 months ago by Ming Tommy Tang ★ 4.7k
0
votes
0
replies
341
views
How to determine which pangenome nodes correspond to hg38 coordinates?
pangenome reference-genome hg38 genomics
8 months ago by a5864557 ▴ 10
0
votes
0
replies
329
views
LDhat analysis pipeline
recombination LDhat
8 months ago by chaudharyc61 ▴ 110
2
votes
7
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1.6k
views
6 follow
Parsing error in sam file when converting to bam
samtools bwa fastq bam sam
updated 8 months ago by 153k • written 8 months ago by • 0
4
votes
1
reply
1.1k
views
GATK site filtering: when should I use VQSR or hard filtering?
VQSR GATK
updated 8 months ago by • 0 • written 3.9 years ago by ▴ 270
0
votes
1
reply
541
views
Missing `pro_ref` Folder in PICRUSt2 Default Files
github PICRUSt2
updated 8 months ago by 45k • written 8 months ago by • 0
2
votes
1
reply
575
views
How to Display Metadata on IGV Visualizations
Integrative-Genomics-Viewer IGV
updated 8 months ago by 45k • written 8 months ago by ▴ 10
0
votes
3
replies
793
views
Understanding how to deal with Brain snRNA-seq data
scanpy python single-cell anndata RNA
updated 8 months ago by ★ 4.7k • written 8 months ago by ▴ 200
2
votes
2
replies
806
views
RNA-seq combined treatment interaction experiment design
RNA-seq DESeq2
updated 8 months ago by 45k • written 8 months ago by ▴ 10
0
votes
0
replies
816
views
Forum: Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping variants
updated 8 months ago by 153k • written 8 months ago by 6.1k
23
votes
11
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21k
views
6 follow
CIBERSORT deconvolution advice
CIBERSORT CIBERSORTx deconvolution
updated 8 months ago by • 0 • written 5.5 years ago by ▴ 150
0
votes
1
reply
778
views
News: In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
Transcriptomics Workshop RNA-Seq
8 months ago by ecSeq Bioinformatics ▴ 20
0
votes
0
replies
392
views
Sesame Data ExperimentHub and related issues
caching sesame methylation
updated 8 months ago by 153k • written 8 months ago by ▴ 10
0
votes
0
replies
439
views
Unable to link peaks to genes for multiomics data
multiome multiomics linkPeaks Signac 10X
8 months ago by sribas.chowdhury888 • 0
0
votes
0
replies
342
views
GWAS for Klebsiella isolates
technical help GWAS
8 months ago by Bahnie • 0
0
votes
0
replies
377
views
CoCoRV - Which file from gnomAD as control
Variants Rare WES
8 months ago by andrebolerbarros • 0
2
votes
1
reply
621
views
SNP/kb in chromosome wise
Variant SNP Calling
updated 8 months ago by 166k • written 8 months ago by ▴ 60
0
votes
0
replies
301
views
time to event GWAS
signals independent
updated 8 months ago by 153k • written 8 months ago by • 0
3
votes
9
replies
1.4k
views
single-cell zeros handling, inputation and filtration
zeros single-cell
updated 8 months ago by ★ 19k • written 8 months ago by • 0
0
votes
3
replies
948
views
submitting to SRA database
files pod5 SRA
updated 8 months ago by 89k • written 8 months ago by ▴ 60
4
votes
3
replies
866
views
Flattened TSS enrichment x unique fragments from scATAC experiment
ATAC
updated 8 months ago by ★ 19k • written 8 months ago by • 0
2
votes
6
replies
1.1k
views
determine softmask regions from FASTA
BED FASTA softmask
updated 8 months ago by 15k • written 8 months ago by ▴ 130
0
votes
4
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1.1k
views
Number of reads supporting a structural variant value in Dragen structural variant calling output
Structural VCF variants Manta
updated 8 months ago by 4.2k • written 8 months ago by ▴ 20
3
votes
2
replies
938
views
Strategy for mapping rat and human gene symbols from scRNA-seq data - dealing with inconsistent nomenclature
Orthologs scRNAseq
updated 8 months ago by 89k • written 8 months ago by • 0
0
votes
0
replies
490
views
News: online course: R/Bioconductor for Mass Spectrometry and Proteomics
Bioconductor R Spectrometry Mass Proteomics
8 months ago by Physalia-courses ★ 2.6k
4
votes
5
replies
912
views
What is the interpretation of sequence enrichment in whole genome sequencing?
sequencing WGS enrichment
updated 8 months ago by 153k • written 8 months ago by ▴ 760
2
votes
9
replies
2.1k
views
Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the same as in the bam headers! (targets: 10575 from the bam vs 67331 from t…
binning metagenomics metabat2
8 months ago by samdegregori • 0
0
votes
0
replies
307
views
Combining expression and mutation data from TCGA
TCGA
updated 8 months ago by 6.5k • written 8 months ago by • 0
0
votes
1
reply
1.0k
views
Annotate .fcs files with gated population classification
FACS Flow Cytometry FlowJo
updated 8 months ago by • 0 • written 4.9 years ago by ▴ 30
0
votes
0
replies
315
views
Converting map & ped files to binary file. Missing info
Map Ped plink
updated 8 months ago by 45k • written 8 months ago by • 0
121,907 results • Page 41 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
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