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801 results • Page 4 of 17
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0
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0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 29 days ago by 43k • written 5.0 years ago by ▴ 140
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 28 days ago by 43k • written 5.1 years ago by ▴ 60
3
votes
0
replies
1.1k
views
Tool: Sars-Cov-2 Genome & ACE 2 Exploration
sequence alignment SNP genome
12 days ago by Ibrahim Tanyalcin ★ 1.2k
0
votes
3
replies
1.1k
views
Discrepancy between E() Values in Blastp Search - HELP
BLAST E-value Blastp Protein
updated 29 days ago by 43k • written 5.4 years ago by • 0
1
vote
4
replies
1.1k
views
Filtering qscore on dorado
dorado filtering QC nanopore Guppy
14 days ago by eebloom ▴ 80
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq DESeq2 DNA-contamination
22 days ago by DKA ▴ 40
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.4 years ago by ▴ 360
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma machine-learning batch-effect
updated 28 days ago by 43k • written 3.8 years ago by 19k
2
votes
11
replies
999
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 18 days ago by ★ 1.2k • written 29 days ago by • 0
2
votes
3
replies
995
views
Method to detect genome doubling
CNV genome doubling
updated 24 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
5
replies
954
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 17 days ago by ★ 2.0k • written 2.1 years ago by • 0
1
vote
8
replies
945
views
Adding CB tag to bam file
samtools bam
updated 22 days ago by 161k • written 28 days ago by • 0
2
votes
7
replies
942
views
Removing duplicates
duplicates ONT minimap2
updated 28 days ago by ▴ 580 • written 29 days ago by • 0
3
votes
9
replies
941
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 28 days ago by ★ 2.4k • written 29 days ago by • 0
7
votes
16
replies
939
views
How many reads for WGS Sequencing?
WGS Bacterial-Genomics
18 days ago by Ruqaiya • 0
2
votes
9
replies
938
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 23 days ago by 4.2k • written 7 months ago by • 0
13
votes
14
replies
907
views
High Malat-1 expression in single cell data
single-cell
updated 9 days ago by ▴ 40 • written 17 days ago by ▴ 40
1
vote
10
replies
888
views
error to run rnammer
phylogenomics rRNA_extraction rnammer
updated 11 days ago by • 0 • written 4 months ago by ▴ 30
4
votes
11
replies
881
views
Redirection of Duplicate PMIDs
pubmed pmid
updated 23 days ago by 4.2k • written 24 days ago by • 0
0
votes
2
replies
862
views
AGeNT LocatIt
AGeNT LocatIt WES UMI duplicates
updated 22 days ago by ★ 2.1k • written 2.8 years ago by ▴ 10
2
votes
3
replies
844
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 12 days ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
842
views
How to compare differentially expressed genes among different affymatrix dataset
microarray batch-effect R
updated 29 days ago by 43k • written 4.8 years ago by ▴ 30
0
votes
1
reply
835
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 28 days ago by 43k • written 3.7 years ago by • 0
1
vote
5
replies
805
views
RNA seq differential expression analysis
RNA-seq normalization
updated 27 days ago by ★ 1.7k • written 29 days ago by • 0
4
votes
6
replies
802
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
0
votes
1
reply
801
views
cnetplot category names are too long
clusterprofiler RNA-Seq enrichplot cnetplot
updated 14 days ago by 43k • written 2.7 years ago by • 0
1
vote
3
replies
793
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 15 hours ago by ▴ 90 • written 2.7 years ago by ▴ 80
2
votes
5
replies
785
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 26 days ago by ▴ 770 • written 27 days ago by ★ 2.4k
1
vote
5
replies
784
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
0
votes
1
reply
782
views
Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq R cellassign batch-effect
updated 18 days ago by ▴ 10 • written 3.3 years ago by ▴ 30
1
vote
4
replies
769
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 28 days ago by 43k • written 4 months ago by • 0
0
votes
3
replies
766
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 17 days ago by • 0 • written 21 months ago by • 0
4
votes
8
replies
763
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs BED eqtl bedtools
updated 20 days ago by 35k • written 21 days ago by ▴ 10
10
votes
14
replies
762
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 9 days ago by 142k • written 15 days ago by • 0
5
votes
3
replies
758
views
Illumina reads preprocessing best practice for snp calling applications
Illumina snp
updated 27 days ago by • 0 • written 10 months ago by ▴ 310
3
votes
6
replies
752
views
Ciriquant not configuring hisat2 indexed files
ciriquant
25 days ago by Atul K. • 0
3
votes
3
replies
751
views
KissDE and batch effect
kissDE kissplice
24 days ago by david.b.rombaut ▴ 10
8
votes
8
replies
750
views
PCA plot (Suggestions Needed)
DESeq2 PCAplot
updated 22 days ago by 14k • written 23 days ago by ▴ 10
0
votes
2
replies
745
views
homer not configured properly
Homer makeTagDirectory
updated 14 days ago by • 0 • written 24 months ago by • 0
3
votes
4
replies
744
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
24 days ago by rahu • 0
0
votes
0
replies
741
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 28 days ago by 43k • written 3.5 years ago by ▴ 180
1
vote
6
replies
725
views
anRichment is missing
WGCNA anRichment
updated 10 days ago by 142k • written 6 months ago by ▴ 180
2
votes
4
replies
719
views
Count all variants from vcf file
variants vcf Count
updated 10 days ago by 161k • written 21 months ago by • 0
5
votes
4
replies
718
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
28 days ago by BioinfGuru ★ 1.7k
5
votes
4
replies
711
views
How to compare the quality of assemblies
nextdenovo assembly hifiasm pacbio
23 days ago by kirillkirilenko ▴ 40
0
votes
11
replies
710
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
21 days ago by atowns21 • 0
0
votes
1
reply
703
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 16 days ago by 43k • written 16 days ago by • 0
0
votes
3
replies
696
views
Pluritest for pluripotency broken
pluripotent pluritest cells stem
updated 8 days ago by ▴ 20 • written 21 months ago by • 0
2
votes
9
replies
694
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 9 days ago by • 0
3
votes
8
replies
678
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 10 days ago by ▴ 410 • written 14 days ago by ▴ 100
801 results • Page 4 of 17
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Recent Replies
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input? by LucisTheFather • 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank you
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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