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121,903 results • Page 29 of 2439
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366
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Help with the interpretation of Silhouette width averaging
clustering kmeans cluster silhouettemethod
6 months ago by Maria Jose • 0
0
votes
1
reply
1.0k
views
Job: Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Cancer Oncology Tenure-earning Faculty Bioinformatics
updated 6 months ago by 153k • written 6 months ago by • 0
0
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1
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1.0k
views
Job: Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Oncology Faculty Leadership
updated 6 months ago by 153k • written 6 months ago by • 0
2
votes
2
replies
658
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Pre-Alignment process
read_depth_measure
6 months ago by AIMAR ▴ 70
0
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0
replies
424
views
Differential methylation analysis using Dorado
dorado m6A DRS nanopore
6 months ago by baibhu1234 ▴ 60
0
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0
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340
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Annotate Phylogentic Tree with classes
python tree phylogenetic analysis
6 months ago by BIANCA • 0
1
vote
1
reply
515
views
Is it possible for genomic DNA to be sequenced in a modern RNA-seq protocol?
transcriptome genome RNA-seq
updated 6 months ago by 153k • written 6 months ago by ★ 2.1k
4
votes
3
replies
747
views
Picard gives empty value for HS_LIBRARY_SIZE when running CollectHsMetrics
sequencing library picard
6 months ago by Bertalan_Takacs ▴ 140
1
vote
2
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597
views
single cell compositional analysis - how adjusting for covariates (age)
compositional-analysis RNA-seq single-cell
6 months ago by Francesco ▴ 20
0
votes
1
reply
616
views
Differential Expression Analysis of scRNA seq data with Pseudobulking
edgeR scrnaseq pseudobulking
updated 6 months ago by 89k • written 6 months ago by • 0
0
votes
0
replies
408
views
News: Last Two Spots Available – R/Bioconductor for Mass Spectrometry & Proteomics
Proteomics Bioconductor Mass-Spectrometry R
updated 6 months ago by 45k • written 6 months ago by ★ 2.6k
0
votes
0
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383
views
News: Last-Minute Open Spots for Our RNA-Seq Workshops!
single-cell transcriptomics scRNAseq RNAseq
updated 6 months ago by 45k • written 6 months ago by ▴ 20
2
votes
2
replies
829
views
advice on rooting a tree in R
R tree ggtree phylo
6 months ago by Matteo Ungaro ▴ 130
0
votes
1
reply
404
views
Beagle removed many sites in the target dataset after imputation
genotype beagle imputation
6 months ago by LCG • 0
0
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0
replies
363
views
Blog: Novogene Single-cell and Spatial Multi-omics Case Study: Application in Immunosenescence
Single-cell
6 months ago by Novogene ▴ 510
0
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2
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1.4k
views
ArchR error Error in grid.Call.graphics(C_downvppath, name$path, name$name, strict): Viewport 'Norm. Enrichment -log10(P-adj) [0-Max]_heatmap_body_1_…
ArchR
6 months ago by Bioinformatics_16 • 0
3
votes
5
replies
7.9k
views
normalization to "housekeeping" genes of RNAseq data vs qPCR result
qPCR RNAseq
updated 6 months ago by • 0 • written 4.1 years ago by ▴ 40
0
votes
12
replies
1.4k
views
MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genome
reference-genome
updated 6 months ago by 153k • written 6 months ago by • 0
4
votes
8
replies
3.3k
views
6 follow
Normalizing TCR data
Analysis
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 20
0
votes
1
reply
462
views
Alternative normalization strategy for RNA-seq data with global downregulation
DESeq2 RNA-seq GeneExpression Normalization miRNA
updated 6 months ago by 89k • written 6 months ago by • 0
1
vote
2
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535
views
Extract Fungal mRNA reda from RNASeq Sample
rnaseq rna fungus bbsplit.sh transcriptomics
6 months ago by SomeOne ▴ 240
0
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0
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472
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cNMF missing spectra iterations - what am I doing wrong?
cNMF python single-cell
6 months ago by yura.grabovska ▴ 820
0
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0
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318
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Repeated sequences
Repetitive sequences
6 months ago by frarodmar17 • 0
3
votes
7
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1.0k
views
Best way to assess relatedness of eukaryotic organisms from sequencing reads?
phylogenomics phylogenetics ngs kmer sequencing
updated 6 months ago by 7.9k • written 6 months ago by ▴ 60
1
vote
0
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330
views
Potential Contamination in ARG Metagenomic Analysis – How to Filter Out Reads?
metagenomics ARG
6 months ago by JH ▴ 10
1
vote
2
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1.1k
views
Negative coverage depths when running jgi_summarize_bam_contig_depths (Metabat2)
assembly metagenome Metabat
6 months ago by amir.rakhimov.b • 0
0
votes
0
replies
339
views
How to interpret this RNA-seq multi-peak distribution density plot?
rna-seq distribution
6 months ago by Omar • 0
0
votes
2
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747
views
Salmon RNA-Seq transcript quantification
Salmon RNA-Seq
updated 6 months ago by 7.1k • written 6 months ago by • 0
0
votes
0
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401
views
News: Course: Comparative Genomics (ONLINE; April 7-11)
Comparative-Genomics SV SNV Genome-Annotation
updated 6 months ago by 45k • written 6 months ago by ★ 2.6k
0
votes
1
reply
618
views
Discrepancy in GEO2R vs. Raw Data Analysis: Significance of DEGs
Raw-Data-Analysis Microarray GEO2R Probe-IDs
updated 6 months ago by 89k • written 6 months ago by ▴ 20
0
votes
5
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923
views
DiffBind Normalization ATAC-Seq Question: When to drop a sample?
ATAC-Seq DiffBind
6 months ago by John • 0
3
votes
2
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617
views
Freelance career advice
freelance job career
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
0
replies
284
views
Pathways Logic
Logic Reactome Netlist
6 months ago by sciwiseg • 0
3
votes
2
replies
699
views
CNV detection
ressources CNV Large_Cohort computation
updated 6 months ago by ★ 4.3k • written 6 months ago by ▴ 10
0
votes
0
replies
296
views
cfRNA-seq data
cfRNA-Seq
6 months ago by frarodmar17 • 0
1
vote
2
replies
557
views
fastq direction
bioinfo
6 months ago by gagi1993 • 0
5
votes
4
replies
795
views
Seeking chloroplast and mitochondrial reference for barley
barley chloroplast reference mitochondrial genome
updated 6 months ago by ▴ 10 • written 6 months ago by ▴ 100
1
vote
2
replies
726
views
Help with Reproducing Global Bird Migration Flyway Map in R
R Flyway Map offtopic
updated 6 months ago by ★ 2.9k • written 6 months ago by ▴ 50
7
votes
8
replies
2.2k
views
Tool: Fast, flexible grep for very large FASTQ files
grepq grep-like FASTQ
6 months ago by milesforjazz ▴ 70
1
vote
1
reply
523
views
Changing order of elements on Chord diagram in R
Chort Chart R Diagram Plot
updated 6 months ago by ▴ 380 • written 6 months ago by ▴ 70
4
votes
3
replies
767
views
Using other individuals and related species to improve a de novo genome assembly
Illumina
updated 6 months ago by 4.7k • written 6 months ago by ▴ 10
0
votes
2
replies
620
views
Sankey plot for unequal node sizes
R sankey network ggplot
6 months ago by Luca Arbore ▴ 10
0
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0
replies
343
views
Best tools for gene regulatory netweork analysis
time-course network transcriptome RNA-seq
6 months ago by f.tomoyuki • 0
0
votes
4
replies
739
views
Pymol semaglutide structure
Pymol protein PDB Tool structure
6 months ago by Hansen_869 ▴ 80
0
votes
0
replies
324
views
Consensus Peak Shifts after dba_count() and Default Peak Width in DiffBind
DiffBind CHIP-Seq
6 months ago by Siqi ▴ 10
0
votes
1
reply
544
views
Variant Validation Tool for Mouse RNA-seq
mouse variants transcriptome validation
updated 6 months ago by 56k • written 6 months ago by • 0
2
votes
3
replies
1.4k
views
Ensemble Neural Network - Stacking ensemble neural network accuracy is significantly similar or low compared to base models
Neural-network Gradient-boosting Cox Random-forest Ensemble
6 months ago by Yugan Gogul Muthukumar ▴ 10
0
votes
1
reply
507
views
How to analysed RNA Seq for multiple samples
RNA-SEQ Transcriptome
updated 6 months ago by ★ 1.7k • written 6 months ago by • 0
2
votes
5
replies
801
views
Transcriptome Variant Calling Mapping to Introns
mouse introns transcriptome alignment variants
updated 6 months ago by 22k • written 6 months ago by • 0
7
votes
9
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1.3k
views
How to extract a multiple sequence alignment file from a CRAM file?
samtools cram
updated 6 months ago by ★ 4.3k • written 6 months ago by ★ 2.9k
121,903 results • Page 29 of 2439
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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??
Comment: Is this PCA plot correct??
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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…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Thomas.H.Hampton ▴ 10
Thanks again for your carefully considered reply. You asked what I am hoping to learn from a DE analysis. Autologous stem cells are well …
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi ATpoint, thank you very much for the helpful insight! I'm still doing some literature reading on this myself, but have you come across a…
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