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121,889 results • Page 18 of 2438
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News: Online course: Introduction to R and Bioconductor
R Bioconductor Genomics
4 months ago by Physalia-courses ★ 2.6k
0
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0
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334
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IM-fusion data analysis
IM-fusion
4 months ago by frarodmar17 • 0
0
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4
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598
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error in reading codelink data
readcodelinkset
4 months ago by nazaninhoseinkhan ▴ 530
0
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1
reply
505
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R ChIP-seq ENCODE Diffbind
updated 4 months ago by ▴ 390 • written 4 months ago by • 0
7
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5
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1.1k
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY PAR vcf gnomad Pseudoautosomal
updated 4 months ago by ★ 4.3k • written 4 months ago by 166k
8
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6
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3.7k
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News: Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python training
updated 4 months ago by 153k • written 12.4 years ago by 11k
1
vote
1
reply
556
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Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data Breast-Cancer TCGA
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
0
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2
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630
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Kallisto to tximport to deseq2
enseml deseq2 Kallisto
updated 4 months ago by 153k • written 4 months ago by ▴ 160
0
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0
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386
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Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV purity genome ploidy
4 months ago by ting • 0
10
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8
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1.3k
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow workflow pipeline
4 months ago by neng ▴ 50
0
votes
1
reply
510
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What to choose as background in statistic test genetics
test expression gene statistic
updated 4 months ago by ★ 2.9k • written 4 months ago by • 0
5
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4
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860
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differential exon usage from Salmon outputs
edgeR diffSpliceDGE DEU salmon
updated 4 months ago by ★ 8.3k • written 4 months ago by ▴ 10
0
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0
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708
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Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics genetic-variation epistasis snp gnomad
4 months ago by SonicSoal • 0
0
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0
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408
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News: Online course -Reproducibility in Bioinformatics - July 7–9
Singularity Git Docker Snakemake Nextflow
4 months ago by Physalia-courses ★ 2.6k
1
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5
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816
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RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA rna-sequencing
4 months ago by h • 0
0
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3
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642
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 4 months ago by 153k • written 4 months ago by • 0
1
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2
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533
views
Pathway enrichment analysis on time-series data by filtering out age comparisons
pea go rnaseq time-series
4 months ago by fullycratered • 0
6
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10
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1.2k
views
building snpeff database for plant
plant
updated 3 months ago by 15k • written 4 months ago by ▴ 70
1
vote
1
reply
475
views
How to find motif in specific region
motif chip-seq
updated 4 months ago by 36k • written 4 months ago by • 0
0
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0
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418
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How to interpret perplexing qcovhsp result in blastx
blastx qcovhsp blastn
4 months ago by samuel.himes • 0
0
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0
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379
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Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF bcftools
4 months ago by Mwangana • 0
0
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0
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441
views
Best Practices for Integrating RNA-seq Time Series from Multiple Studies with Varying Protocols
differential-expression meta-analysis integration RNA-seq time-series
4 months ago by enee ▴ 20
10
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9
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5.6k
views
bcftools query add header
bcftools
updated 4 months ago by 153k • written 3.5 years ago by ▴ 750
0
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2
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676
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Alternative to PASApipeline
transcriptomics annotation
updated 4 months ago by 7.9k • written 4 months ago by ▴ 160
0
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0
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349
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How to Get a Genetic Map, Given the Physical Position and Genotype Data of Markers
genetic-map
updated 4 months ago by 45k • written 4 months ago by • 0
1
vote
7
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3.0k
views
vcftools --weir-fst-pop returns -nan
fst vcftools
updated 4 months ago by 56k • written 2.8 years ago by • 0
1
vote
3
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653
views
HISAT2 with Cleaned Data
HISAT2 RNASeq
updated 4 months ago by 15k • written 4 months ago by ▴ 10
4
votes
1
reply
557
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Definitions for "differential expression" and "differential abundance" in RNA-seq?
rna-seq deseq abundance differential-expression
updated 4 months ago by 45k • written 4 months ago by • 0
2
votes
5
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831
views
Efficiently find regions in bed file that are within start and end regions of another bed file.
intersect bedtools
updated 4 months ago by 36k • written 4 months ago by • 0
2
votes
4
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659
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16S Libraries With Non-Purified Short Fragments
Sequencing 16S Libraries Magnetic Beads
4 months ago by alenew.am ▴ 10
0
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1
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563
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How to map polyA tails to barcodes in paired end reads for single cell RNA-seq
RNA-seq cell polyA single
updated 4 months ago by 153k • written 4 months ago by ▴ 10
7
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6
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5.5k
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Questions related to ChromHMM+using MACS2 peak calling output bed file as input for ChromHMM?
macs2 ChIP-Seq ChromHMM MACS2 CHROMHMM
updated 4 months ago by ▴ 10 • written 6.3 years ago by ▴ 120
4
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5
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1.0k
views
Editing and Adding to a GTF file
Annotation Gene-ID GTF
updated 4 months ago by 45k • written 4 months ago by ▴ 10
4
votes
2
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558
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Averaging multiple IgG BAM files for use as a control in ChromHMM
ChromHMM bam averag
updated 4 months ago by 89k • written 4 months ago by ▴ 10
3
votes
3
replies
805
views
Deduplication rate of shotgun metagenomes using fastqc
metagenome fastqc shotgun deduplication
updated 4 months ago by 7.9k • written 4 months ago by • 0
0
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0
replies
391
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News: online course: Introduction to Genome Annotation
Gene-Prediction Genome-Annotation Gene-Models
4 months ago by Physalia-courses ★ 2.6k
0
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2
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1.7k
views
ValueError: Found array with 0 sample(s) (shape=(0, 138)) while a minimum of 1 is required. In metawrap - concoct binning module
concoct metawrap module
4 months ago by shevch2009 ▴ 20
6
votes
7
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1.2k
views
Circular heatmap using circos.heatmap in R
R circos heatmap circularheatmap
updated 4 months ago by 153k • written 4 months ago by ▴ 30
0
votes
0
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388
views
Zebrafish phenotype ontology enrichment analyses
ontology zebrafish
4 months ago by Li • 0
0
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2
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563
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Sequence Duplication for Single-End 3RAD Data
duplication reduced-representation
4 months ago by Sarah • 0
1
vote
6
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1.5k
views
6 follow
Not retrieving Mitochondrial Genes in Single Cell analysis
single-cell
updated 4 months ago by 45k • written 14 months ago by ▴ 10
0
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0
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390
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News: Ancient Metagenomics course - online, May 27-29
ancient-metagenomics aDNA aMeta
4 months ago by Physalia-courses ★ 2.6k
0
votes
1
reply
534
views
Issues running scAPAtrap
scAPAtrap polyA scRNAseq
updated 4 months ago by 153k • written 4 months ago by ▴ 10
5
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3
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695
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What are BED files?
BED
updated 4 months ago by 36k • written 4 months ago by • 0
3
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8
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1.0k
views
ggplot make boxplots more wide
ggplot2 r
4 months ago by Nona ▴ 90
2
votes
1
reply
542
views
Minimum number of samples for multi-omics data integration
multi-omics
updated 4 months ago by 45k • written 4 months ago by ▴ 10
1
vote
0
replies
444
views
News: Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation workshop UConn
4 months ago by zsc25001 ▴ 10
1
vote
1
reply
550
views
Assigning a string variable on Visual Studio using python
python visual-studio
updated 4 months ago by 45k • written 4 months ago by • 0
4
votes
4
replies
956
views
Tool: Gene Exons Painter
Genomics Visualisation Exons Transcripts Isoforms
updated 4 months ago by 4.2k • written 4 months ago by ▴ 70
0
votes
0
replies
491
views
News: Course online:Functional programming in R, May 27-30
R programming functional
4 months ago by soledad.esteban • 0
121,889 results • Page 18 of 2438
Recent Votes
Answer: activity of unloaded/unassembled Tn5
Comment: Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs
Answer: Yeast reference-based genome assembly
Comment: Is this PCA plot correct??
Comment: How to load sam.gz files on IGV?
Comment: How to load sam.gz files on IGV?
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Recent Replies
Comment: Yeast reference-based genome assembly by GenoMax 153k
> The gene originates from yeast, What does this mean? Are you putting a gene from a different genus/species into some other yeast? Can yo…
Comment: Variant analysis for mouse WES by alba • 0
Hi, thanks for the suggestion! I’m aware of Ensembl VEP, and in fact, I already have my VCFs annotated with VEP. The challenge I’m facing i…
Answer: Structural Variant identification on pangenome graphs by colindaven 7.9k
There might be something here for you : https://github.com/colindaven/awesome-pangenomes Otherwise, I know creating a pangenome with `mi…
Comment: replace gene names in gff file by ja569116 • 0
Hi @juke34 Is it possible to specify the prefix/ custom gene name to rename all the genes in the gff3 file with AGAT, so that the differen…
Answer: Yeast reference-based genome assembly by colindaven 7.9k
Nanopore reads are long enough to create a full assembly. Why not first try to create a whole genome assembly with a tool like Flye if you …
Comment: Variant analysis for mouse WES by alba • 0
I saw that but it looks like it only works for trinucleotideMatrix() specifically, I was looking to be able to generate rainfallPlot(), for…
Comment: RTG (Real Time Genomics) docker image - Problem dealing with different VCFs by stuckinanendlessfebruary ▴ 10
Dr. Jeremy, Thank you sincerely for your time! I wanted to close the loop: the issue appears to have been the RTG Tools Docker image versi…
Answer: Conversion of Gene Name to Ensembl ID by Thanujay S • 0
Hey! A bit late to the party! I’ve built a simple wrapper (named SESC) around biomaRt to streamline Ensembl ID conversions. It supports bot…
Comment: Variant analysis for mouse WES by barslmn ★ 2.4k
You can try Ensembl VEP which can also annotate organism other than human.
Comment: Variant analysis for mouse WES by GenoMax 153k
> I’d like to analyze using a package similar to maftools. Looks like `maftools` works with mouse data: https://github.com/PoisonAlien/ma…
Comment: Is this PCA plot correct?? by GenoMax 153k
It would also help to add information about what kind of data this is and what you did to the data to get to this point.
Comment: How to load sam.gz files on IGV? by marongiu.luigi ▴ 760
I can now see the alignment, thank you.
Comment: How to load sam.gz files on IGV? by marongiu.luigi ▴ 760
Thank you, it worked!
Comment: Fungal Genome Assembly: In a messed up situation by SomeOne ▴ 240
HI, Just to add some information here. I tried that merging of Hifi + ONT data then assembly using hifiasm --ont. It didnot work as expect…
Comment: Is this PCA plot correct?? by dthorbur ★ 3.1k
In addition to these comments, I would suggest checking other PCs, the first two PCs only explain a combined 39% of the variance. Since you…
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