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13,167 results • Page
4 of 264
Sort: Views
Rank
Views
Votes
Replies
28
votes
7
replies
19k
views
6 follow
VCF merge or concatenate?
snp
VCF
VCFTools
written 4.8 years ago by
rokragna295
▴ 60
38
votes
21
replies
19k
views
8 follow
Tool:
pybam - 100% python BAM reader
python
htspython
bam
pysam
updated 10 months ago by
Ram
43k • written 8.1 years ago by
John
13k
176
votes
46
replies
19k
views
26 follow
Forum:
Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by
Istvan Albert
100k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
8
votes
6
replies
19k
views
Converting gtf format to bed format
bed
updated 4 months ago by
Apex92
▴ 280 • written 9.6 years ago by
thjnant
▴ 160
15
votes
9
replies
19k
views
8 follow
How to count fasta sequences efficiently using (or not ) biopython
biopython
python
fasta
updated 6 months ago by
Mark
★ 1.5k • written 6.3 years ago by
juan.crescente
▴ 110
3
votes
8
replies
19k
views
Downloading gtf file for RefSeq
RNA-Seq
RefSeq
GTF
updated 4 months ago by
xiaoleiusc
▴ 140 • written 6.6 years ago by
KVC_bioinfo
▴ 590
26
votes
9
replies
19k
views
8 follow
Favorite Splice Site Prediction/Evaluation Tools
splicing
prediction
updated 11 months ago by
abhilashdasari.10
▴ 30 • written 11.5 years ago by
Alex Paciorkowski
3.5k
38
votes
26
replies
19k
views
16 follow
GO analysis: DAVID vs GREAT vs GOrilla
RNA-Seq
ChIP-Seq
GO
gene ontology
written 8.2 years ago by
biostart
▴ 370
13
votes
7
replies
18k
views
Running STAR aligner on paired-end reads as single-end read
RNA-Seq
paired end
single end
STAR
align
updated 5 months ago by
xiaoleiusc
▴ 140 • written 5.8 years ago by
Glory Basumata
▴ 140
6
votes
5
replies
18k
views
7 follow
How different is rlog transformation from vst transformation in DESeq2
DESeq2
count normalization
updated 9 months ago by
ATpoint
82k • written 5.6 years ago by
piyushjo
▴ 700
55
votes
6
replies
18k
views
Decoy In Reference Assembly
1000genomes
updated 12 months ago by
kmzhou4
• 0 • written 11.0 years ago by
Sangwoo Kim
▴ 440
13
votes
13
replies
18k
views
9 follow
How Do I Translate Multiple (More Than 25000) Dna Sequences With Different Frames To Protein Seuquence?
dna
protein
updated 4 weeks ago by
ummeswaiba
• 0 • written 10.3 years ago by
biostar
▴ 170
38
votes
12
replies
18k
views
8 follow
BEDOPS gtf2bed conversion error with Ensembl GTF
gtf2bed
ensembl
bedops
gtf
updated 10 weeks ago by
Alex Reynolds
35k • written 7.8 years ago by
bioinformatics.cancer
▴ 260
18
votes
10
replies
18k
views
Regarding Split reads and discordant reads
genome
sequence
sequencing
alignment
updated 12 months ago by
Ram
43k • written 6.6 years ago by
DL
▴ 50
1
vote
2
replies
18k
views
Forum:
Would you rather analyze a dataset with a strong, non-collinear batch effect, or a weak, collinear batch effect.
collinear
latent
batch-effect
variable
GLM
9 months ago by
LauferVA
4.2k
6
votes
9
replies
18k
views
HISAT2 software installation
RNA-Seq
updated 3 months ago by
GenoMax
142k • written 6.7 years ago by
saj98
▴ 140
12
votes
11
replies
17k
views
Trying to get genome for bedtools
genome
updated 9 months ago by
mg
▴ 250 • written 7.8 years ago by
radwa.raed
▴ 40
21
votes
11
replies
17k
views
the problem with rpkm (and tpm)
RNA-Seq
next-gen
gene-expression
normalization
updated 10 months ago by
Chris
▴ 280 • written 9.6 years ago by
user123456
▴ 180
9
votes
10
replies
17k
views
8 follow
Forum:
Open Source Bioinformatics projects for beginners
Open-Source
Beginners
updated 3 months ago by
Saransh
• 0 • written 6.3 years ago by
Eugenia84
▴ 40
65
votes
24
replies
17k
views
14 follow
Mapping Snps To Pathways
snp
genotyping
pathway
gene
enrichment
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Pierre Lindenbaum
161k
8
votes
6
replies
17k
views
News:
Bioinformatics PhD Programs in the US
education
PhD
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Ahmed Youssef
▴ 70
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 5 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
20
votes
10
replies
17k
views
Could you please explain Fold change, % of change, and log2 fold change (L2FC) to a layment?
gene
RNA-Seq
next-gen
fold-change
updated 8 months ago by
Ram
43k • written 4.5 years ago by
WUSCHEL
▴ 760
17
votes
9
replies
17k
views
6 follow
Tool:
ggrepel: repel overlapping text labels in ggplot2
R
visualization
updated 11 months ago by
Ram
43k • written 8.3 years ago by
Kamil
★ 2.3k
3
votes
9
replies
17k
views
8 follow
Module to RMSD two proteins with Python?
python
protein-structure
updated 10 months ago by
Aleksandr
• 0 • written 8.4 years ago by
bef1
• 0
12
votes
11
replies
16k
views
10 follow
Retrieve The Reads And Fastq From Bam File
samtools
updated 7 months ago by
Reem
• 0 • written 11.6 years ago by
rehma.ar
▴ 290
21
votes
6
replies
16k
views
survfit(Surv()) P-value interpretation for 3 survival curves?
survfit
Surv
survival curves
R
updated 7 weeks ago by
marshelma
• 0 • written 4.6 years ago by
JJDollar
▴ 130
27
votes
6
replies
16k
views
Tool:
Bioawk - Fasta, Fastq, Sam, Bed, Gff Aware Awk Programming
awk
updated 10 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
30
votes
18
replies
16k
views
8 follow
Is It Possible For Two Different Affymetrix Probe Set Id To Have Common Annotations To Same Gene ?
microarray
annotation
affymetrix
probeset
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Khader Shameer
18k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression
RNA-Seq
DESeq2
updated 7 weeks ago by
Bionaught
• 0 • written 5.9 years ago by
firestar
★ 1.6k
7
votes
11
replies
16k
views
11 follow
How to generate KEGG pathway classification chart
RNA-Seq
kegg
updated 10 months ago by
microecologist93
▴ 20 • written 5.2 years ago by
dongchenchen
▴ 30
15
votes
34
replies
16k
views
10 follow
Issues installing bcl2fastq?
bcl2fastq
demultiplexing
updated 9 weeks ago by
barslmn
★ 2.1k • written 6.8 years ago by
a.rex
▴ 350
21
votes
7
replies
16k
views
6 follow
GFA to Fasta file
sequence
updated 3 months ago by
Adam Taranto
▴ 40 • written 8.4 years ago by
marcela.uliano
▴ 90
35
votes
10
replies
16k
views
11 follow
Which Chip Seq Peak Callers Do You Use?
chip-seq
peak-calling
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Stew
★ 1.4k
7
votes
14
replies
16k
views
7 follow
Tool:
Art: Simulation Tools To Generate Synthetic Next-Generation Sequencing Reads.
sequence
updated 10 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
68
votes
25
replies
16k
views
12 follow
Tool:
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
fastq
SRA
updated 6 months ago by
GenoMax
142k • written 5.2 years ago by
Phil Ewels
★ 1.4k
12
votes
10
replies
15k
views
6 follow
conversion of GFF3 formate to BED format
RNA-Seq
updated 3 months ago by
Ram
43k • written 5.9 years ago by
blooming.daisy333
▴ 110
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing
gene
rna-seq
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Shahzad
▴ 30
28
votes
4
replies
15k
views
Tool:
Plotting GSEA output in R
RNA-Seq
javaGSEA
GSEA
updated 10 months ago by
Ram
43k • written 7.8 years ago by
thomaskuilman
▴ 850
15
votes
11
replies
15k
views
10 follow
TCGA/Broad Institute CNV Files Segment Mean
tcga
cnv
updated 5 months ago by
sativus
▴ 20 • written 9.7 years ago by
dirigible2012
▴ 320
31
votes
30
replies
15k
views
6 follow
Tool:
BioVinci: user-friendly software to make plotting easy - PCA, 3D scatter plot, venn diagram, you name it.
gene
RNA-Seq
Venn-diagram
PCA
updated 10 months ago by
Ram
43k • written 6.0 years ago by
Jennifer Pham
▴ 450
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software
phylogenetics
visualization
updated 6 months ago by
Ram
43k • written 14.2 years ago by
Roderic Page
▴ 390
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
28
votes
13
replies
15k
views
7 follow
Create Consensus Sequences For Sequence Pairs Within A Multiple Alignment?
consensus
phylogenetics
fasta
multiple-alignment
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Dave Lunt
★ 2.0k
40
votes
6
replies
15k
views
7 follow
Mapping Ensembl Gene IDs with dot suffix
ensembl
gene
biomart
bioconductor
R
updated 9 months ago by
zx8754
11k • written 6.2 years ago by
mk
▴ 290
28
votes
27
replies
15k
views
9 follow
Extracting A Subset Of Sequences From A Fastq File (Biopython Speed)
biopython
python
fastq
next-gen-sequencing
updated 6 months ago by
Ram
43k • written 14.1 years ago by
Darked89
4.6k
17
votes
12
replies
15k
views
10 follow
Converting from BED to SAF/GFF
bed
gff
saf
featureCount
updated 6 months ago by
drperaltaxp
• 0 • written 7.4 years ago by
ccag
▴ 60
18
votes
25
replies
15k
views
13 follow
Easy way to split VCF file by chromosome
sequence
TOPMED
chromosome
Imputation
SNP
updated 10 months ago by
Pierre Lindenbaum
161k • written 2.3 years ago by
ConvolutedGenome
▴ 30
3
votes
5
replies
15k
views
NCBI error report
blastp
alignment
updated 10 months ago by
Ram
43k • written 8.2 years ago by
archana.bioinfo87
▴ 210
13,167 results • Page
4 of 264
Recent Votes
Comment: How to remove multiple batch effects from RNA-seq data before limma differential
Comment: automatic clustering annotation using python
automatic clustering annotation using python
Answer: How to compute TPM normalized values for TCGA miRNA data?
C: Convert .Txt File To Bed File
A: Get nonoverlapping regions of two bed files
Get nonoverlapping regions of two bed files
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Comment: How to convert normalized BigWig file to count matrix?
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feather-W
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Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
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feather-W
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Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
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You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
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This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
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Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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There have been a couple of bugs found that affect imputation accuracy, one in build-kmer-index and one in find-paths. The find-paths bug o…
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Hi, In your samtools flagstat, -o specifies the output format. This can be set to 'default', 'json', or 'tsv'. If -o is not specified , t…
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