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13
votes
6
replies
600
views
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Is training data used exclusively in machine learning
learning machine
updated 14 months ago by 82k • written 14 months ago by ▴ 370
2
votes
2
replies
1.2k
views
Scatter plot of DEG in R
R RNA-seq Bioconductor DEG
15 months ago by ATCG ▴ 370
6
votes
5
replies
1.9k
views
Can someone explain in detail the meaning of a gseaplot in GSEA
gseaplot
updated 17 months ago by ▴ 250 • written 2.3 years ago by ▴ 370
1
vote
1
reply
496
views
RNA-seq batches across different tissues
RNA-Seq Normalization
21 months ago by ATCG ▴ 370
0
votes
0
replies
372
views
RAP-seq datasets but no corresponding RNA-seq
RNA-Seq TRAP-Seq Translation Transcription
21 months ago by ATCG ▴ 370
0
votes
0
replies
542
views
Normalization for RNA-Seq samples
RNA-Seq Tissue specific Transcriptome
22 months ago by ATCG ▴ 370
1
vote
2
replies
533
views
help clarify ways to measure coverage in RNA-Seq libraries
RNA-Seq coverage
2.0 years ago by ATCG ▴ 370
4
votes
6
replies
1.4k
views
Understanding the colData in DESeq2
DEseq2 ColData LFC
2.0 years ago by ATCG ▴ 370
0
votes
2
replies
476
views
over-representation of sequences that map to "Drosophila melanogaster signal recognition particle
RNA-Seq TRAP-Seq FastQC SRP representation
2.0 years ago by ATCG ▴ 370
1
vote
3
replies
630
views
Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq Differential translation
updated 2.0 years ago by 82k • written 2.0 years ago by ▴ 370
1
vote
1
reply
637
views
Ribo-seq data analysis using an RNA-Seq analysis pipeline
RNA-Seq Ribo-Seq TRAP-Seq
updated 2.1 years ago by ★ 3.9k • written 2.1 years ago by ▴ 370
0
votes
0
replies
450
views
Protein annotation tool
Proteins
2.1 years ago by ATCG ▴ 370
7
votes
8
replies
517
views
Change the field separator
R awk field separator
updated 2.1 years ago by ★ 1.2k • written 2.1 years ago by ▴ 370
2
votes
4
replies
1.1k
views
Is it appropriate to apply quantile normalization on RNA-Seq before computing the Pearson correlation?
RNA-Seq Quantile Normalization Correlation
2.2 years ago by ATCG ▴ 370
4
votes
2
replies
2.2k
views
Is it possible to run DESeq with only two replicates in one group?
RNA-Seq DESeq2 Replicates
updated 2.2 years ago by 64k • written 2.2 years ago by ▴ 370
0
votes
10
replies
618
views
Differential gene expression analysis
RNA-Seq DESeq2
updated 2.2 years ago by 12k • written 2.2 years ago by ▴ 370
3
votes
5
replies
1.1k
views
How to estimate the inter sample and inter replicate correlation coefficient?
RNA-Seq Replicates R2 Correlation coefficients
2.3 years ago by ATCG ▴ 370
5
votes
2
replies
803
views
How to subset DESeq2 results
DESEq2 GSEA
updated 2.3 years ago by 12k • written 2.3 years ago by ▴ 370
2
votes
4
replies
1.4k
views
Gene set enrichment analysis input data
GSE DESeq2
2.3 years ago by ATCG ▴ 370
1
vote
1
reply
725
views
Infer strandedness of my single-end RNA-Seq data
RNA-Seq HISAT2 strandedness
updated 2.3 years ago by ★ 3.9k • written 2.3 years ago by ▴ 370
17
votes
26
replies
1.1k
views
File conversion in bash, discrepancy in number of lines after conversion.
file conversion csv txt
updated 2.3 years ago by 11k • written 2.3 years ago by ▴ 370
4
votes
5
replies
1.9k
views
ReactomePA enrichPathway function
ReactomePA enrichPathway
2.3 years ago by ATCG ▴ 370
1
vote
6
replies
548
views
Filter fastq files
Fastq trimmomatic
updated 2.3 years ago by 94k • written 2.3 years ago by ▴ 370
0
votes
2
replies
720
views
over-represented is not removed after trimmomatic
trimmomatic fastqc
2.3 years ago by ATCG ▴ 370
2
votes
2
replies
566
views
Is indexing a genome the same as annotating a genome?
samtools index genome indexing
2.3 years ago by ATCG ▴ 370
2
votes
4
replies
3.8k
views
DESeq2 Error: package or namespace load failed for 'DESeq2'
RNA-Seq DESeq2 image not found
updated 2.3 years ago by 4.0k • written 2.3 years ago by ▴ 370
2
votes
2
replies
2.3k
views
Do illumina instruments generate four fastq files per sample?
Fasq Illumina lane
updated 2.3 years ago by 119k • written 2.3 years ago by ▴ 370
2
votes
4
replies
596
views
How to recognize single-end fastq files
RNA-Seq Fastq single-end
updated 2.3 years ago by 119k • written 2.3 years ago by ▴ 370
5
votes
2
replies
847
views
Pathway vs Network
Pathway Networks RNA-Seq
updated 2.3 years ago by 15k • written 2.3 years ago by ▴ 370
8
votes
8
replies
899
views
Drosophila reference genomes
genome Drosophila Model organisms Annotation
updated 2.3 years ago by 119k • written 2.3 years ago by ▴ 370
0
votes
2
replies
3.0k
views
Download NCBI GEO dataset
RNA-Seq GEO GSE
updated 2.4 years ago by ▴ 540 • written 2.4 years ago by ▴ 370
0
votes
3
replies
809
views
Extracting related sequences from a FASTA file
Sequence comparizon Data mining kmer
updated 3.6 years ago by 20 • written 3.7 years ago by ▴ 370
1
vote
3
replies
3.0k
views
Filter out related individuals from a vcf file using Plink or Hail
Hail Plink VCF
updated 3.7 years ago by 11k • written 4.7 years ago by ▴ 370
4
votes
6
replies
1.5k
views
Bulk primer design
primers bulk FASTA kmer
updated 3.7 years ago by 147k • written 3.7 years ago by ▴ 370
1
vote
4
replies
799
views
where to keep scripts for new software
$PATH Unix install
3.9 years ago by ATCG ▴ 370
3
votes
3
replies
1.8k
views
GMAP download page
RNA-Seq GMAP PacBio
3.9 years ago by ATCG ▴ 370
5
votes
8
replies
2.0k
views
differential gene expression analysis
confounders RNA-Seq Limma EdgeR Regression
4.3 years ago by ATCG ▴ 370
0
votes
2
replies
784
views
number of individuals in each genotype group for a particular SNP
plink SNP
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 370
1
vote
1
reply
1.1k
views
missing a sample and individual attributes in GTEX Adipose- Subcutaneous(v7)
RNA-Seq GTEx Adipose
4.5 years ago by ATCG ▴ 370
0
votes
1
reply
1.4k
views
remove lowly expressed genes by selecting genes that had FPKM > 0
RNA-Seq filter
4.6 years ago by ATCG ▴ 370
0
votes
1
reply
1.7k
views
PCA from genotype data using the --pca option in plink2
pca plink2 LD pruning PCA
4.6 years ago by ATCG ▴ 370
2
votes
2
replies
1.2k
views
extract a chromosome region from vcf.c1.GRU.tar
vcf .tar
4.6 years ago by ATCG ▴ 370
0
votes
5
replies
981
views
available subcutaneous adipose RNA-seq
RNA-Seq Subcutaneous adipose
updated 4.6 years ago by ★ 3.9k • written 4.6 years ago by ▴ 370
1
vote
1
reply
1.4k
views
bash loop to align 366 RNAseq samples in individual folders
RNA-Seq Bash Unix STAR alignment
4.6 years ago by ATCG ▴ 370
1
vote
3
replies
1.9k
views
vcf file filter
filter vcf SNPs minor allele homozygotes
updated 4.8 years ago by 147k • written 4.8 years ago by ▴ 370
1
vote
1
reply
1.7k
views
FastQTL-Finding a candidate QTL per phenotype
FastQTL
4.9 years ago by ATCG ▴ 370
0
votes
0
replies
936
views
veqtl-mapper in a replication study --perm option
veqtl-mapper permutations replication LD
4.9 years ago by ATCG ▴ 370
1
vote
1
reply
1.5k
views
sea corrected expression matrix
batch effects microarrays sva
5.1 years ago by ATCG ▴ 370
1
vote
1
reply
1.4k
views
sequencing QC metrics from kallisto
kallisto
5.4 years ago by ATCG ▴ 370
0
votes
0
replies
1.8k
views
HOMER: how to plot xy scatter plots
ChIP-Seq HOMER XY scatter plot
5.7 years ago by ATCG ▴ 370
52 results • Page 1 of 2
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