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868 results • Page 6 of 18
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4
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294
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Genbank File Format
gbkformat
16 days ago by alenew.am • 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 28 days ago by 43k • written 18 months ago by • 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 29 days ago by 43k • written 4.7 years ago by ▴ 10
1
vote
4
replies
1.4k
views
Comparing RNA-Seq data to online databases
RNA-Seq batch-effect
updated 29 days ago by 43k • written 4.7 years ago by ▴ 10
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq batch-effect deseq
updated 28 days ago by 43k • written 2.3 years ago by • 0
6
votes
4
replies
432
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
14 days ago by Estevão ▴ 10
1
vote
4
replies
483
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 22 days ago by • 0 • written 6 months ago by • 0
0
votes
4
replies
299
views
Correlation Analysis
statistics methylation NGS expression
5 days ago by Researcher ▴ 30
0
votes
4
replies
212
views
Sequencing Depth (Read Depth) Calculations
depth
20 hours ago by LucisTheFather • 0
6
votes
4
replies
2.3k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 29 days ago by • 0 • written 4.6 years ago by ▴ 40
1
vote
4
replies
337
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 1 day ago by 8.6k • written 3 days ago by ▴ 30
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 21 days ago by • 0 • written 2.5 years ago by • 0
0
votes
4
replies
3.6k
views
SNPEff database building error
SNP
updated 3 days ago by • 0 • written 7.1 years ago by • 0
3
votes
4
replies
310
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 9 hours ago by 142k • written 13 hours ago by 161k
1
vote
4
replies
270
views
Add stats to boxplot in R
stats R
1 day ago by Ghada • 0
0
votes
4
replies
413
views
Highest variable features in single cell data
single-cell
9 days ago by carolofharvest ▴ 40
1
vote
3
replies
427
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
3 days ago by kalavattam ▴ 190
0
votes
3
replies
297
views
bcftools - reducing to "sites-only"?
sites-only bcftools
updated 7 days ago by 161k • written 8 days ago by • 0
0
votes
3
replies
561
views
JASPAR2024_getMatrixSet error
JASPAR2024 getMatrixSet
updated 7 days ago by 43k • written 12 weeks ago by ▴ 10
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 2 days ago by 43k • written 2 days ago by • 0
4
votes
3
replies
438
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc conda nextflow
updated 19 days ago by 3.2k • written 20 days ago by ▴ 40
3
votes
3
replies
214
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
updated 14 hours ago by 82k • written 1 day ago by • 0
3
votes
3
replies
353
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 2 days ago by ▴ 140 • written 5 days ago by • 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat R SVA Biostatistics batch-effect
updated 28 days ago by 43k • written 7.5 years ago by • 0
2
votes
3
replies
843
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 12 days ago by • 0 • written 7 months ago by • 0
1
vote
3
replies
306
views
Bedtools merge minimum overlap?
bedtools genomics
updated 13 days ago by 35k • written 14 days ago by • 0
7
votes
3
replies
4.6k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 29 days ago by 43k • written 5.2 years ago by ▴ 100
1
vote
3
replies
259
views
Help with Biopython for Beginner
Python ORF FASTA Biopython
updated 7 days ago by 142k • written 8 days ago by • 0
0
votes
3
replies
253
views
RNAseq RNA content
mRNA Linux rRNA RNA-seq RNA
updated 2 days ago by ▴ 580 • written 2 days ago by ▴ 10
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 21 days ago by • 0 • written 22 months ago by ▴ 180
1
vote
3
replies
6.2k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 29 days ago by 43k • written 5.6 years ago by ▴ 170
0
votes
3
replies
340
views
Snakemake wrapper issue
fastqc snakemake
updated 2 days ago by • 0 • written 9 weeks ago by • 0
1
vote
3
replies
779
views
About runing Pilon on individual chromosomes when polish draft genome assembly
Pilon chromosome polish genome draft
updated 4 hours ago by ▴ 90 • written 2.7 years ago by ▴ 80
1
vote
3
replies
334
views
some error in building kraken2 database
metagenome kraken2
22 days ago by Art1ess • 0
0
votes
3
replies
443
views
How to identify gaps in a genome?
awk seqkit assembly fasta genome
updated 23 days ago by 6.4k • written 4 weeks ago by • 0
3
votes
3
replies
550
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 26 days ago by 14k • written 27 days ago by ▴ 580
0
votes
3
replies
313
views
KEGG Pathways
r RNA-seq
updated 16 days ago by 43k • written 16 days ago by • 0
0
votes
3
replies
349
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
3 days ago by mropri ▴ 150
2
votes
3
replies
381
views
clustalo - align milions of short seq, memory issue
memory clustalo
updated 24 days ago by ★ 27k • written 24 days ago by ▴ 120
2
votes
3
replies
275
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
3 days ago by Azra ▴ 10
3
votes
3
replies
579
views
Korean human genome reference file
GWAS reference imputation
27 days ago by SeoGyun • 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
3
replies
271
views
Finding variants within a subset of a BAM file
variant calling
2 days ago by ramiro.barrantes • 0
0
votes
3
replies
248
views
Software to separate reads from different individuals
software development nanopore
updated 17 days ago by 142k • written 17 days ago by ▴ 20
0
votes
3
replies
319
views
Difference between samtools "-f 9" and "-f 11"
samtools sam bam
updated 23 days ago by 100k • written 23 days ago by • 0
1
vote
3
replies
436
views
Limma compare between 3 conditions vs 2 conditions
Limma
updated 29 days ago by ★ 7.2k • written 7 weeks ago by ▴ 280
2
votes
3
replies
499
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
28 days ago by valentinatsar • 0
2
votes
3
replies
334
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 7 days ago by ★ 2.4k • written 11 days ago by ▴ 60
1
vote
3
replies
448
views
PCA plot
DESeq2 PCAplot
updated 18 days ago by 4.2k • written 21 days ago by ▴ 10
1
vote
3
replies
361
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf tabix bcftools
updated 29 days ago by 161k • written 5 weeks ago by • 0
868 results • Page 6 of 18
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Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
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ATAC-seq sample normalization
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
Answer: --normalizeUsing RPGC
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Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty by Jordan M Eizenga ▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly by sansan_96 ▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by e.r.zakiev ▴ 210
Very good question and analysis. I personally only tried SoupX so can't weigh in on the comparison. This might be not really the issue here…
Comment: Is there any way to modify this pie chart ? by marco.barr ▴ 120
Try following the same logic as the guide which adds the labels about halfway through each pie slice value. Check column's name in script b…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
sorry for that, this is first time i use it.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank sir, i will check it again
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